From fa8f225e6c3d3df4bdc03029b1598201d079b387 Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 29 Jan 2026 13:41:27 -0800 Subject: [PATCH 01/17] create_term_entry fix for RDF3.0;fix: issue with virtuoso graphs included in the query --- lib/ncbo_annotator.rb | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/lib/ncbo_annotator.rb b/lib/ncbo_annotator.rb index 5f69c43..54dcaa5 100644 --- a/lib/ncbo_annotator.rb +++ b/lib/ncbo_annotator.rb @@ -412,7 +412,7 @@ def annotate(text, options={}) if expand_with_mappings expand_mappings(annotations, ontologies) end - return annotations.values + annotations.values end def annotate_direct(text, options={}) @@ -555,6 +555,9 @@ def expand_hierarchies(annotations, levels, ontologies) id = sol[:id].to_s parent = sol[:parent].to_s ontology = sol[:graph].to_s + # fix: issue with virtuoso graphs included in the query + next unless ontology.include?("ontologies") + ontology = ontology[0..ontology.index("submissions")-2] id_group = ontology + id @@ -602,7 +605,7 @@ def expand_mappings(annotations, ontologies) def get_prefixed_id_from_value(instance_prefix, val) # NCBO-696 - Remove case-sensitive variations on terms in annotator dictionary intId = unsigned_to_signed(XXhash.xxh64(val.upcase, 112233)) - return get_prefixed_id(instance_prefix, intId) + get_prefixed_id(instance_prefix, intId) end ## @@ -661,11 +664,12 @@ def redis_last_mgrep_restart_default_timestamp() def create_term_entry(redis, instance_prefix, ontResourceId, resourceId, label_type, val, semanticTypes) begin # NCBO-696 - Remove case-sensitive variations on terms in annotator dictionary - val.to_s.upcase!() - rescue ArgumentError => e + val = val.dup.upcase + rescue ArgumentError + val = val.dup # NCBO-832 - SCTSPA Annotator Cache building error (UTF-8) val = val.encode('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '') - val.to_s.upcase!() + val = val.upcase end # exclude single-character or empty/null values @@ -679,7 +683,7 @@ def create_term_entry(redis, instance_prefix, ontResourceId, resourceId, label_t # always append them back to the original value semanticTypeCodes = get_semantic_type_codes(semanticTypes) semanticTypeCodes = (semanticTypeCodes.empty?) ? "" : - "#{DATA_TYPE_DELIM}#{semanticTypeCodes}" + "#{DATA_TYPE_DELIM}#{semanticTypeCodes}" matches = redis.hget(id, resourceId) if (matches.nil?) @@ -709,16 +713,15 @@ def get_semantic_type_codes(semanticTypes) semanticTypeCodes << val i += 1 end - return semanticTypeCodes + semanticTypeCodes end def get_prefixed_id(instance_prefix, intId) - return "#{IDPREFIX.call(instance_prefix)}#{intId}" + "#{IDPREFIX.call(instance_prefix)}#{intId}" end def mappings_for_class_ids(class_ids) - mappings = LinkedData::Mappings.mappings_for_classids(class_ids) - return mappings + LinkedData::Mappings.mappings_for_classids(class_ids) end def hierarchy_query(class_ids) @@ -726,14 +729,13 @@ def hierarchy_query(class_ids) # if an ID is not of the proper URI format class_ids.select! { |id| id =~ /\A#{URI::regexp}\z/ } filter_ids = class_ids.map { |id| "?id = <#{id}>" } .join " || " - query = < ?parent . } FILTER (#{filter_ids}) FILTER (!isBlank(?parent)) FILTER (?parent != ) } eos - return query end end end From a3f45dc497ec8188872a3ed15cdade44d5f3fd64 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 16:06:51 -0800 Subject: [PATCH 02/17] updated Gemfile to point to updated goo and ontologies_linked_data --- Gemfile | 7 ++-- Gemfile.lock | 107 ++++++++++++++++++++++++++++++++------------------- 2 files changed, 70 insertions(+), 44 deletions(-) diff --git a/Gemfile b/Gemfile index fc7515f..057d129 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,5 @@ source 'https://rubygems.org' -gem 'cube-ruby' gem 'faraday' gem 'ffi' gem 'oj', '~> 3.0' @@ -15,6 +14,6 @@ group :development do end # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'goo', github: 'ncbo/goo', branch: 'develop' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' -gem 'sparql-client', github: 'ncbo/sparql-client', tag: 'v6.3.0' +gem 'goo', github: 'ncbo/goo', branch: 'ontoportal-lirmm-development' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'chore/ontoportal-lirmm-goo-compat' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development' diff --git a/Gemfile.lock b/Gemfile.lock index bc272d9..362a384 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,14 +1,16 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 87a21a76bc61392d0629a19c8a18593f606b52e5 - branch: develop + revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d + branch: ontoportal-lirmm-development specs: goo (0.0.2) addressable (~> 2.8) pry - rdf (= 1.0.8) + rdf + rdf-raptor + rdf-rdfxml + rdf-vocab redis - request_store rest-client rsolr sparql-client @@ -16,12 +18,13 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a90ae62dcc2bee43600f056946598900190e9346 - branch: develop + revision: d9aefd5a9bff4fcb40d687b16b25e171457deeeb + branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) activesupport bcrypt + down (~> 5.0) goo json libxml-ruby @@ -33,17 +36,16 @@ GIT rack rack-test rsolr - rubyzip + rubyzip (~> 3.0) GIT remote: https://github.com/ncbo/sparql-client.git - revision: 512edc320b43e83971835dc046b4923485e8f70e - tag: v6.3.0 + revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 + branch: ontoportal-lirmm-development specs: - sparql-client (1.0.1) - json_pure (>= 1.4) - net-http-persistent (= 2.9.4) - rdf (>= 1.0) + sparql-client (3.2.2) + net-http-persistent (~> 4.0, >= 4.0.2) + rdf (~> 3.2, >= 3.2.11) GEM remote: https://rubygems.org/ @@ -54,18 +56,20 @@ GEM multi_json (~> 1.3) thread_safe (~> 0.1) tzinfo (~> 0.3.37) - addressable (2.8.7) - public_suffix (>= 2.0.2, < 7.0) - bcrypt (3.1.20) + addressable (2.8.8) + public_suffix (>= 2.0.2, < 8.0) + bcp47_spec (0.2.1) + bcrypt (3.1.21) bigdecimal (3.1.9) builder (3.3.0) coderay (1.1.3) - concurrent-ruby (1.3.5) - connection_pool (2.5.3) - cube-ruby (0.0.3) - date (3.4.1) + concurrent-ruby (1.3.6) + connection_pool (3.0.2) + date (3.5.1) docile (1.4.1) domain_name (0.6.20240107) + down (5.4.2) + addressable (~> 2.8) faraday (2.12.2) faraday-net_http (>= 2.0, < 3.5) json @@ -75,18 +79,21 @@ GEM ffi (1.17.1-aarch64-linux-gnu) ffi (1.17.1-arm64-darwin) ffi (1.17.1-x86_64-linux-gnu) + htmlentities (4.4.2) http-accept (1.7.0) - http-cookie (1.0.8) + http-cookie (1.1.0) domain_name (~> 0.5) i18n (0.9.5) concurrent-ruby (~> 1.0) + io-console (0.8.2) json (2.10.1) - json_pure (2.8.1) - libxml-ruby (5.0.4) + libxml-ruby (5.0.5) + link_header (0.0.8) logger (1.6.6) macaddr (1.7.2) systemu (~> 2.6.5) - mail (2.8.1) + mail (2.9.0) + logger mini_mime (>= 0.1.1) net-imap net-pop @@ -95,17 +102,18 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2025.0715) + mime-types-data (3.2026.0127) mini_mime (1.1.5) minitest (4.7.5) - multi_json (1.15.0) - net-ftp (0.3.8) + multi_json (1.19.1) + net-ftp (0.3.9) net-protocol time net-http (0.6.0) uri - net-http-persistent (2.9.4) - net-imap (0.5.9) + net-http-persistent (4.0.8) + connection_pool (>= 2.2.4, < 4) + net-imap (0.6.2) date net-protocol net-pop (0.1.2) @@ -126,19 +134,39 @@ GEM pry (0.15.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (6.0.1) - rack (3.1.16) + public_suffix (7.0.2) + rack (3.2.4) rack-test (2.2.0) rack (>= 1.3) rake (10.5.0) - rdf (1.0.8) - addressable (>= 2.2) + rdf (3.3.4) + bcp47_spec (~> 0.2) + bigdecimal (~> 3.1, >= 3.1.5) + link_header (~> 0.0, >= 0.0.8) + logger (~> 1.5) + ostruct (~> 0.6) + readline (~> 0.0) + rdf-raptor (3.2.0) + ffi (~> 1.15) + rdf (~> 3.2) + rdf-rdfxml (3.3.0) + builder (~> 3.2, >= 3.2.4) + htmlentities (~> 4.3) + rdf (~> 3.3) + rdf-xsd (~> 3.3) + rdf-vocab (3.3.3) + rdf (~> 3.3) + rdf-xsd (3.3.0) + rdf (~> 3.3) + rexml (~> 3.2) + readline (0.0.4) + reline redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.25.1) + redis-client (0.26.4) connection_pool - request_store (1.7.0) - rack (>= 1.4) + reline (0.6.3) + io-console (~> 0.5) rest-client (2.1.0) http-accept (>= 1.7.0, < 2.0) http-cookie (>= 1.0.2, < 2.0) @@ -149,7 +177,7 @@ GEM builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) ruby-xxHash (0.4.0.2) - rubyzip (2.4.1) + rubyzip (3.2.2) simplecov (0.22.0) docile (~> 1.1) simplecov-html (~> 0.11) @@ -161,9 +189,9 @@ GEM simplecov_json_formatter (0.1.4) systemu (2.6.5) thread_safe (0.3.6) - time (0.4.1) + time (0.4.2) date - timeout (0.4.3) + timeout (0.6.0) tzinfo (0.3.62) uri (1.0.3) uuid (2.3.9) @@ -176,7 +204,6 @@ PLATFORMS x86_64-linux DEPENDENCIES - cube-ruby faraday ffi goo! From c14909e966475106ed1c66f17745e8aef78d4ff0 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 16:56:16 -0800 Subject: [PATCH 03/17] updated to ruby 3.2 and minitest 6 --- .ruby-version | 2 +- Gemfile | 10 +- Gemfile.lock | 221 -------------------------------------- Rakefile | 1 + lib/ncbo_annotator.rb | 1 + test/test_annotator.rb | 4 +- test/test_case.rb | 53 ++++----- test/test_mgrep_client.rb | 4 +- 8 files changed, 42 insertions(+), 254 deletions(-) delete mode 100644 Gemfile.lock diff --git a/.ruby-version b/.ruby-version index 9cec716..be94e6f 100644 --- a/.ruby-version +++ b/.ruby-version @@ -1 +1 @@ -3.1.6 +3.2.2 diff --git a/Gemfile b/Gemfile index 057d129..74549b7 100644 --- a/Gemfile +++ b/Gemfile @@ -3,11 +3,15 @@ source 'https://rubygems.org' gem 'faraday' gem 'ffi' gem 'oj', '~> 3.0' -gem 'rake', '~> 10.0' +gem 'rake' +gem 'request_store' +gem 'parallel' gem 'ruby-xxHash' +gem 'activesupport' -group :development do - gem 'minitest', '~> 4.0' +group :test do + gem 'minitest' + gem 'minitest-reporters' gem 'pry' gem 'simplecov' gem 'simplecov-cobertura' # for codecov.io diff --git a/Gemfile.lock b/Gemfile.lock deleted file mode 100644 index 362a384..0000000 --- a/Gemfile.lock +++ /dev/null @@ -1,221 +0,0 @@ -GIT - remote: https://github.com/ncbo/goo.git - revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d - branch: ontoportal-lirmm-development - specs: - goo (0.0.2) - addressable (~> 2.8) - pry - rdf - rdf-raptor - rdf-rdfxml - rdf-vocab - redis - rest-client - rsolr - sparql-client - uuid - -GIT - remote: https://github.com/ncbo/ontologies_linked_data.git - revision: d9aefd5a9bff4fcb40d687b16b25e171457deeeb - branch: chore/ontoportal-lirmm-goo-compat - specs: - ontologies_linked_data (0.0.1) - activesupport - bcrypt - down (~> 5.0) - goo - json - libxml-ruby - multi_json - net-ftp - oj - omni_logger - pony - rack - rack-test - rsolr - rubyzip (~> 3.0) - -GIT - remote: https://github.com/ncbo/sparql-client.git - revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 - branch: ontoportal-lirmm-development - specs: - sparql-client (3.2.2) - net-http-persistent (~> 4.0, >= 4.0.2) - rdf (~> 3.2, >= 3.2.11) - -GEM - remote: https://rubygems.org/ - specs: - activesupport (4.0.13) - i18n (~> 0.6, >= 0.6.9) - minitest (~> 4.2) - multi_json (~> 1.3) - thread_safe (~> 0.1) - tzinfo (~> 0.3.37) - addressable (2.8.8) - public_suffix (>= 2.0.2, < 8.0) - bcp47_spec (0.2.1) - bcrypt (3.1.21) - bigdecimal (3.1.9) - builder (3.3.0) - coderay (1.1.3) - concurrent-ruby (1.3.6) - connection_pool (3.0.2) - date (3.5.1) - docile (1.4.1) - domain_name (0.6.20240107) - down (5.4.2) - addressable (~> 2.8) - faraday (2.12.2) - faraday-net_http (>= 2.0, < 3.5) - json - logger - faraday-net_http (3.4.0) - net-http (>= 0.5.0) - ffi (1.17.1-aarch64-linux-gnu) - ffi (1.17.1-arm64-darwin) - ffi (1.17.1-x86_64-linux-gnu) - htmlentities (4.4.2) - http-accept (1.7.0) - http-cookie (1.1.0) - domain_name (~> 0.5) - i18n (0.9.5) - concurrent-ruby (~> 1.0) - io-console (0.8.2) - json (2.10.1) - libxml-ruby (5.0.5) - link_header (0.0.8) - logger (1.6.6) - macaddr (1.7.2) - systemu (~> 2.6.5) - mail (2.9.0) - logger - mini_mime (>= 0.1.1) - net-imap - net-pop - net-smtp - method_source (1.1.0) - mime-types (3.7.0) - logger - mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0127) - mini_mime (1.1.5) - minitest (4.7.5) - multi_json (1.19.1) - net-ftp (0.3.9) - net-protocol - time - net-http (0.6.0) - uri - net-http-persistent (4.0.8) - connection_pool (>= 2.2.4, < 4) - net-imap (0.6.2) - date - net-protocol - net-pop (0.1.2) - net-protocol - net-protocol (0.2.2) - timeout - net-smtp (0.5.1) - net-protocol - netrc (0.11.0) - oj (3.16.10) - bigdecimal (>= 3.0) - ostruct (>= 0.2) - omni_logger (0.1.4) - logger - ostruct (0.6.1) - pony (1.13.1) - mail (>= 2.0) - pry (0.15.2) - coderay (~> 1.1) - method_source (~> 1.0) - public_suffix (7.0.2) - rack (3.2.4) - rack-test (2.2.0) - rack (>= 1.3) - rake (10.5.0) - rdf (3.3.4) - bcp47_spec (~> 0.2) - bigdecimal (~> 3.1, >= 3.1.5) - link_header (~> 0.0, >= 0.0.8) - logger (~> 1.5) - ostruct (~> 0.6) - readline (~> 0.0) - rdf-raptor (3.2.0) - ffi (~> 1.15) - rdf (~> 3.2) - rdf-rdfxml (3.3.0) - builder (~> 3.2, >= 3.2.4) - htmlentities (~> 4.3) - rdf (~> 3.3) - rdf-xsd (~> 3.3) - rdf-vocab (3.3.3) - rdf (~> 3.3) - rdf-xsd (3.3.0) - rdf (~> 3.3) - rexml (~> 3.2) - readline (0.0.4) - reline - redis (5.4.1) - redis-client (>= 0.22.0) - redis-client (0.26.4) - connection_pool - reline (0.6.3) - io-console (~> 0.5) - rest-client (2.1.0) - http-accept (>= 1.7.0, < 2.0) - http-cookie (>= 1.0.2, < 2.0) - mime-types (>= 1.16, < 4.0) - netrc (~> 0.8) - rexml (3.4.1) - rsolr (2.6.0) - builder (>= 2.1.2) - faraday (>= 0.9, < 3, != 2.0.0) - ruby-xxHash (0.4.0.2) - rubyzip (3.2.2) - simplecov (0.22.0) - docile (~> 1.1) - simplecov-html (~> 0.11) - simplecov_json_formatter (~> 0.1) - simplecov-cobertura (2.1.0) - rexml - simplecov (~> 0.19) - simplecov-html (0.13.1) - simplecov_json_formatter (0.1.4) - systemu (2.6.5) - thread_safe (0.3.6) - time (0.4.2) - date - timeout (0.6.0) - tzinfo (0.3.62) - uri (1.0.3) - uuid (2.3.9) - macaddr (~> 1.0) - -PLATFORMS - aarch64-linux - arm64-darwin-22 - arm64-darwin-23 - x86_64-linux - -DEPENDENCIES - faraday - ffi - goo! - minitest (~> 4.0) - oj (~> 3.0) - ontologies_linked_data! - pry - rake (~> 10.0) - ruby-xxHash - simplecov - simplecov-cobertura - sparql-client! - -BUNDLED WITH - 2.4.22 diff --git a/Rakefile b/Rakefile index e6c18cf..f40d4cf 100644 --- a/Rakefile +++ b/Rakefile @@ -2,6 +2,7 @@ require 'rake/testtask' Rake::TestTask.new do |t| t.libs = [] + t.warning = false t.test_files = FileList['test/**/test*.rb'] end diff --git a/lib/ncbo_annotator.rb b/lib/ncbo_annotator.rb index 54dcaa5..d2cbc49 100644 --- a/lib/ncbo_annotator.rb +++ b/lib/ncbo_annotator.rb @@ -10,6 +10,7 @@ require 'logger' require 'benchmark' require 'ruby-xxhash' +require 'active_support/core_ext/object/blank' require_relative 'annotation' require_relative 'ncbo_annotator/mgrep/mgrep' require_relative 'ncbo_annotator/config' diff --git a/test/test_annotator.rb b/test/test_annotator.rb index 58ca971..3f36f01 100644 --- a/test/test_annotator.rb +++ b/test/test_annotator.rb @@ -77,7 +77,7 @@ def test_generate_dictionary_file assert class_pages.length > 100, "No classes in system ???" annotator = Annotator::Models::NcboAnnotator.new annotator.generate_dictionary_file - assert File.exists?(Annotator.settings.mgrep_dictionary_file), "The dictionary file did not get created successfully" + assert File.exist?(Annotator.settings.mgrep_dictionary_file), "The dictionary file did not get created successfully" lines = File.readlines(Annotator.settings.mgrep_dictionary_file) cur_inst = annotator.redis_current_instance() @@ -102,7 +102,7 @@ def test_generate_dictionary_file end def test_mallet_recognizer - skip "Skipping Mallet recognizer test because the core Java APIs are not present" unless (File.exists?($ncbo_annotator_project_bin + "mallet.jar")) + skip "Skipping Mallet recognizer test because the core Java APIs are not present" unless (File.exist?($ncbo_annotator_project_bin + "mallet.jar")) count, acronyms, cogpo = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ ont_count: 1, diff --git a/test/test_case.rb b/test/test_case.rb index aa9817f..1f65234 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -36,48 +36,51 @@ $stdout.flush end -require 'minitest/unit' -MiniTest::Unit.autorun +require 'minitest/autorun' -class AnnotatorUnit < MiniTest::Unit - - def self.ontologies - @@ontologies +class AnnotatorUnit + class << self + attr_accessor :ontologies end - def before_suites + def self.setup_once + return if @setup_done + + @setup_done = true # code to run before the very first test LinkedData::SampleData::Ontology.delete_ontologies_and_submissions - @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true) - @@sty = LinkedData::SampleData::Ontology.load_semantic_types_ontology(process_submission: true) + self.ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true) + LinkedData::SampleData::Ontology.load_semantic_types_ontology(process_submission: true) annotator = Annotator::Models::NcboAnnotator.new annotator.init_redis_for_tests - annotator.create_term_cache_from_ontologies(@@ontologies, true) + annotator.create_term_cache_from_ontologies(ontologies, true) annotator.redis_switch_instance - end - def after_suites - # code to run after the very last test - LinkedData::SampleData::Ontology.delete_ontologies_and_submissions + Minitest::Runnable.runnables.each do |suite| + suite.before_suite if suite.respond_to?(:before_suite) + end end +end - def _run_suites(suites, type) - before_suites - super(suites, type) - ensure - after_suites +module AnnotatorTestSetup + def before_setup + AnnotatorUnit.setup_once + super end +end - def _run_suite(suite, type) - suite.before_suite if suite.respond_to?(:before_suite) - super(suite, type) - ensure +Minitest::Test.prepend(AnnotatorTestSetup) + +Minitest.after_run do + Minitest::Runnable.runnables.each do |suite| suite.after_suite if suite.respond_to?(:after_suite) end + + # code to run after the very last test + LinkedData::SampleData::Ontology.delete_ontologies_and_submissions end -MiniTest::Unit.runner = AnnotatorUnit.new ## # Base test class. Put shared test methods or setup here. -class TestCase < MiniTest::Unit::TestCase +class TestCase < Minitest::Test end diff --git a/test/test_mgrep_client.rb b/test/test_mgrep_client.rb index 2760bc1..7a70ca6 100644 --- a/test/test_mgrep_client.rb +++ b/test/test_mgrep_client.rb @@ -1,10 +1,10 @@ require "pry" -require "minitest/unit" +require "minitest/autorun" require_relative "../lib/ncbo_annotator.rb" require_relative "../config/config.rb" -class TestMgrepClient < MiniTest::Unit +class TestMgrepClient < Minitest::Test def test_mgrep client = Annotator::Mgrep::Client.new(Annotator.settings.mgrep_host, Annotator.settings.mgrep_port, Annotator.settings.mgrep_alt_host, Annotator.settings.mgrep_alt_port) From 7a419a6f5775aa75bea7160b27abe68c4d3395c5 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 16:57:18 -0800 Subject: [PATCH 04/17] Gemfile.lock update --- Gemfile.lock | 361 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 361 insertions(+) create mode 100644 Gemfile.lock diff --git a/Gemfile.lock b/Gemfile.lock new file mode 100644 index 0000000..902f7c3 --- /dev/null +++ b/Gemfile.lock @@ -0,0 +1,361 @@ +GIT + remote: https://github.com/ncbo/goo.git + revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d + branch: ontoportal-lirmm-development + specs: + goo (0.0.2) + addressable (~> 2.8) + pry + rdf + rdf-raptor + rdf-rdfxml + rdf-vocab + redis + rest-client + rsolr + sparql-client + uuid + +GIT + remote: https://github.com/ncbo/ontologies_linked_data.git + revision: d9aefd5a9bff4fcb40d687b16b25e171457deeeb + branch: chore/ontoportal-lirmm-goo-compat + specs: + ontologies_linked_data (0.0.1) + activesupport + bcrypt + down (~> 5.0) + goo + json + libxml-ruby + multi_json + net-ftp + oj + omni_logger + pony + rack + rack-test + rsolr + rubyzip (~> 3.0) + +GIT + remote: https://github.com/ncbo/sparql-client.git + revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 + branch: ontoportal-lirmm-development + specs: + sparql-client (3.2.2) + net-http-persistent (~> 4.0, >= 4.0.2) + rdf (~> 3.2, >= 3.2.11) + +GEM + remote: https://rubygems.org/ + specs: + activesupport (8.1.2) + base64 + bigdecimal + concurrent-ruby (~> 1.0, >= 1.3.1) + connection_pool (>= 2.2.5) + drb + i18n (>= 1.6, < 2) + json + logger (>= 1.4.2) + minitest (>= 5.1) + securerandom (>= 0.3) + tzinfo (~> 2.0, >= 2.0.5) + uri (>= 0.13.1) + addressable (2.8.8) + public_suffix (>= 2.0.2, < 8.0) + ansi (1.5.0) + base64 (0.3.0) + bcp47_spec (0.2.1) + bcrypt (3.1.21) + bigdecimal (3.3.1) + builder (3.3.0) + coderay (1.1.3) + concurrent-ruby (1.3.6) + connection_pool (3.0.2) + date (3.5.1) + docile (1.4.1) + domain_name (0.6.20240107) + down (5.4.2) + addressable (~> 2.8) + drb (2.2.3) + faraday (2.14.0) + faraday-net_http (>= 2.0, < 3.5) + json + logger + faraday-net_http (3.4.2) + net-http (~> 0.5) + ffi (1.17.3) + ffi (1.17.3-aarch64-linux-gnu) + ffi (1.17.3-aarch64-linux-musl) + ffi (1.17.3-arm-linux-gnu) + ffi (1.17.3-arm-linux-musl) + ffi 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sha256=8daf828cc77bcf7d63b0e3bdb6caa47e2272dcfaf4fbfe46f8c3a9df087a829b + uri (1.1.1) sha256=379fa58d27ffb1387eaada68c749d1426738bd0f654d812fcc07e7568f5c57c6 + uuid (2.3.9) sha256=aec0cf592053cd6e07c13c1ef94c440aba705f22eb1ee767b39631f2760124d7 + +BUNDLED WITH + 4.0.5 From 16ecaa954d0d6140dfad7b5fb38ddb19f04b419c Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 18:43:39 -0800 Subject: [PATCH 05/17] removed unused test ontology files --- config/config.test.rb | 4 +- test/data/ontology_files/BRO_v3.2.owl | 4879 --- .../CellLine_OWL_BioPortal_v1.0.owl | 31835 ---------------- 3 files changed, 2 insertions(+), 36716 deletions(-) delete mode 100644 test/data/ontology_files/BRO_v3.2.owl delete mode 100644 test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl diff --git a/config/config.test.rb b/config/config.test.rb index bfba7b9..c33e281 100644 --- a/config/config.test.rb +++ b/config/config.test.rb @@ -13,8 +13,8 @@ REDIS_PORT = ENV.include?('REDIS_PORT') ? ENV['REDIS_PORT'] : 6379 MGREP_HOST = ENV.include?('MGREP_HOST') ? ENV['MGREP_HOST'] : 'localhost' MGREP_PORT = ENV.include?('MGREP_PORT') ? ENV['MGREP_PORT'] : 55556 -SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr/term_search_core1" -SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr/prop_search_core1" +SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" +SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" LinkedData.config do |config| diff --git a/test/data/ontology_files/BRO_v3.2.owl b/test/data/ontology_files/BRO_v3.2.owl deleted file mode 100644 index d298496..0000000 --- a/test/data/ontology_files/BRO_v3.2.owl +++ /dev/null @@ -1,4879 +0,0 @@ - - - - - - - - - - Deprecated for BRO v2.7 - Expertise - - - - A resource as an expert (http://en.wikipedia.org/wiki/Expert) who can answer questions, provide technical assistance, etc. - - - - - - - A resource that provides data from any biomaterial sample that was given to the service provider. This can also be a service that performs an experiment such as electrophysiological examination of LTP in a transgenic mouse. Viewing this as an input/output relationship the input would be a tissue or an animal and the output would be data. - Biomaterial Analysis Service - - - A resource that provides long-term storage for backup copies of files or for files that are no longer in active use, and the ability to retrieve backed up content in the event of a disaster that impacts the system in question, - - - - - - - - - - - Deprecated for BRO v3.0 - Backup Archives and Disaster Recovery - - - Resource - An entity that provides access (either in the open community or within an organization) to material, intellectual, financial, technological, or electronic means of carrying out research and development. - - - - - - Lexical Analysis - Resource that provides access to applications, libraries, or software that converts a sequence of characters into a sequence of tokens. - - - Web Posting - Resources that are disseminated on the Internet via HTTP, FTP and other web protocols. - - - - - - - - - - - - Biochemical (http://en.wikipedia.org/wiki/Biochemistry) supplies provided for a laboratory (http://en.wikipedia.org/wiki/Laboratory) - Deprecated for BRO v2.7 - Biochemical Supply Resource - - - - Deprecated for BRO v2.7 - - - - - Software development - - - - - - - - - - - - Processing Pipeline - Resource that provides access to software, applications, or toolkits that enable execution processing. - - - Methods used in the medical specialty of surgery, as defined in http://en.wikipedia.org/wiki/Surgical_procedure - - - - Surgical Procedure - - - - - - A resource that provides a network model that includes nodes and edges based on physical interactions between the entities represented by the nodes. - Interaction Network - - - - - - Sequence Alignment - Resource that provides access to software, applications, or toolkits that compare two or more genomic sequences and provides summary information. - - - Data Visualization - - - - Resource that provides access to software, applications, or toolkits that present information as an image. - - - Resource that provides access to software, applications, or toolkits that use controllers in the performance of a simulation. - - - - Controllers - - - Resource that provides access to software, applications, or toolkits that perform detection, extraction, representation and analysis of cortical brain structure. - - - - Cortical Modeling - - - Resource that provides access to Software that contains data encoded in binary form and contains instructions for the computer to perform a given set of tasks. - - - - - Binary Executable - - - - Deprecated for BRO v3.0 - - - A resource that provides access to or support for a system of interconnected computers able to share information. - Network and Communication - - - - - - - A data object that has infinite numbers of possible values. Quantitative data is often continuous such as weight, blood pressure. - Deprecated for BRO v3.0 - - - - Continuous Data - - - - - - - - - Visualization - Resource that provides access to tools for graphical, interactive, multimodal and multidimensional data and result visualization. - - - - - - Resource that provides access to software, applications, or toolkits that can be used to specifically model RNA structure and function., - RNA Model - - - A resource that provides access to a written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers. - Book - - - - - - Cross-Sectional Viewer - - - - Resource that provides access to data visualization tools relying on displays of lower-dimensional cross-sectional (hyper)planes. - - - Resource that provides access to software, applications, or toolkits that general data transformations. - Data Transform - - - - - - - - - Resource that provides access to general (hyper)volume visualization tools (e.g., volume rendering). - Manifold Viewer - - - A resource the provides access to papers and/or talk and poster abstracts that are presented at a conference. - Conference Proceeding - - - - - - Flow Cytometry Cell Sorting Facility - A facility or core devoted to analysis of cells by suspension of the cells in a stream of fluid and passing them by an electronic detection apparatus (flow cytometer). - pending final vetting: consider changing name to Flow Cytometry Facility - - - - - - - Graph Viewers - General graph visualization resources - Deprecated for BRO v2.7 - - - - - - - - - - - - - - - - A resource that provides access to instructions regarding how software operates or how to use it. - Software Documentation - Deprecated for BRO v3.0 - - - A resource that provides support for computer-related services such as database hosting and backup and disaster recovery. - Computational Service - - - - - - Code Profiler - - - - A resource that provides a performance analysis tool that measures the behavior of a program as it executes, particularly the frequency and duration of function calls. The profiling process helps to determine which subroutines (or just snippets of code) take longest to execute and which subroutines are called most often. Code profilers are used when you suspect that some part of your code is called very often and maybe there is a need to optimize it, which could significantly improve the overall performance. Profilers use a wide variety of techniques to collect data, including hardware interrupts, code instrumentation, instruction set simulation, operating system hooks, and performance counters. - - - Resource that provides access to software distribution that access to a computer program file or collection of files. - - - Deprecated for BRO v3.0 - - - - - - - - Software Distribution - - - - - - A resource that provides access to structured data that is formatted according to the Resource Description Framework, a language for representing information about resources in the World Wide Web. - RDF Data - - - Computational Biology - - - - As defined in http://en.wikipedia.org/wiki/Computational_biology - - - - - - A collection of tables, charts, or plates to illustrate anatomical structures. - - Deprecated for BRO v3.0 - - - - Anatomic Atlas - - - Proteomics - - - - The large-scale study of proteins - - - PDE Solver - A resource that provides access to a tool or function that generates the solution of a partial differential equation subject to appropriate parameters and initial or boundary conditions. - - - - - - - - - Data Compression - Resource that provides access to software, applications, or toolkits that reduces the bits (information units) needed to encode the data. - - - - - - Deprecated for BRO v2.7 - - Clinical Charts - **previously was called Clinical_Charts_eg_Demographics -we think this should be deleted - - - - - - A facility or core that provides services and equipment related to exercise physiology. - Exercise Study Facility - - - - - - - - - - - - Text Mining - Resource that provides access to software, applications, or toolkits that derives information from free text. - - - - - - Next generation of High throughput DNA sequencer (http://en.wikipedia.org/wiki/DNA_sequencing) - Next Generation Sequencer - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - A physiology facility devoted to nutrition (http://en.wikipedia.org/wiki/Nutrition) research - - - - Nutrition Facility - pending final vetting: Refine definition - - - - Deprecated for BRO v2.7 - - - - - - Provenance and Intellectual Property - - - - News - Resource that provides news and RSS feed resources - - - A data resource that delivers its' data by way of a 'database', which involves a structured data store and interrogation methods for data selection. - Data Repository - Database - - - - - - - - - Thesis - A resource that provides access to a document created to summarize research findings associated with the completion of an academic degree. - - - Resource that provides access to educational resources (incl. book, magazines, audio, video, digital streams, etc.), - Education - - - - - - - - - Multibody Dynamics - Resource that provides access to software, applications, or toolkits that can be used to calculate the time course of multibody dynamics. - - - A resource which provides access to tools or functions that compute linear calculations on vector spaces. - Linear Algebra Tool - - - - - - - pending final vetting: propose to deprecate, but replacement term needed since this term is used in annotation - - - - Programmatic Access - - - defined in http://en.wikipedia.org/wiki/Toxicology - - - - Toxicology - - - Finite Element Model - - - - Resource that provides access to software, applications, or toolkits that can be used to generate approximate solutions of partial differential equations. - - - A resource that provides access to educational materials or events, such as courses, workshops or graduate programs. - Training Resource - As per alignment with NIF resource type hierarchy. - - - - Version Information - - - - - - - - - Molecular Model - Resource that provides access to software, applications, or toolkits that calculate time course of physico-chemical model that representation of a molecule or of the arrangement of molecules in a solid substance, with the purpose of visualizing some of its properties, such as the nature and relative positions of its atoms, the chemical bonds between them, the three-dimensional shape of the molecule, and how its shape can change by bending or rotation of the bonds. - - - Deprecated for BRO v3.0 - License and Terms for Use - - - - - - - A license that describes the constraints for using the resource. - - - - Protein-Protein Interaction - - A resource that provides a description of the interaction network of proteins. - - - Course Material - Resource that provides access to educational material that can be used to disseminate information about a course of study. - - - - - Graph Viewer - Resource that provides access to general graph visualization methods. - - - Flatfile Distribution - A resource that provides access to structured data that is found in separate, unlinked files that is accessible via the internet. - - - - - - Resource that provides access to tools for the representation, modeling, analysis and visualization of biological patterns out of data. - - - - Pattern Recognition - - - Semantic Network - - - - Deprecated for BRO v3.0 - - - - - - - - - - - A resource that provides access to documents describing an account, event, situation, or the like, usually as the result of observation, inquiry, etc. - Report - - - - - - Toolkit - - Resource that provides access to software, applications, or toolkits that deliver software or application in toolkit fashion, whereby the kit components can be used independently of each other, or included as part of another program - - - - Deprecated for BRO v3.0 - - - An table that provides a workspace insulated from vibration. - Vibration Isolation Table - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - - - - - - Molecular Trajectory Data - Deprecated for BRO v3.0 - - - - A resource that provides access to kinetic information, usually quantitative, regarding biological system components over time. - - - - - - - Fabrication Facility - A facility core devoted to creating, manufacturing, building or assembling resources used in scientific research. - - - Deprecated for BRO v3.0 - - - - - - - Structured Data - A resource that distributes data that is organized in a purposeful manner - - - - Resource that provides access to an interactive visualization tool that represents variables in a 2-D graph as colors. - Heat Map - - - - Document Structure Parsing - - - - Resource that provides access to applications, libraries, or software that analyze and report on document structure. - - - - - - X-Ray Crystallography Facility - pending final vetting: Refine definition - A molecular biology facility devoted to x-ray crystallography (http://en.wikipedia.org/wiki/X-ray_crystallography) - - - - - - Resource that provides access to software, applications, or toolkits that are used to enable user input of data and display corresponding information. - Interactive Tool - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - An instrument that is used to administer a drug. - Drug Delivery Device - - - Imaging - - pending final vetting: rename this Imaging_Software (at least as it occurs in Software tree)? - Resource that provides access to software, application, or toolkit that enable visualization methods for imaging data. - - - Biostatistics - - - - As defined in http://en.wikipedia.org/wiki/Biostatistics - - - Resource that provides access to software, applications, or toolkits that can be used model a molecular, cellular, organ, or population network. - - - - Network Interaction Model - - - Molecular Trajectories - - - - - - - Deprecated for BRO v2.7 - - - - - - - - - Resource that provides access to software, applications, or toolkits that generate network maps of biological signaling networks based on applying logic and statistics to observations/hypothesis. - Signaling Network Reconstruction - - - - - - As defined in http://en.wikipedia.org/wiki/Nursing - Nursing - - - Management and communications within the laboratory setting (http://www.umuc.edu/programs/undergrad/certificates/lab_mgmt.shtml) - - - - Research Lab Management - - - Resource that provides access to software, applications, or toolkits that can be used to model combined biomechanical and neurological system. - Neuromuscular Model - - - - - - A resource that provides access to facts and/or information, often in the form of rules that describe the knowledge in a logically consistent manner. - Knowledgebase - - - - - - Clinical Data - - - - - - - Any type of data obtained in the course of caring for humans. - - Deprecated for BRO v3.0 - - - - - Non Computational Service - Deprecated for BRO v2.7 - Biomedical Resources which are not predominantly computing (http://en.wikipedia.org/wiki/Computing) in nature. - - - - - - Calorimeter - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. - - - Meshing - - - - Resource that provides access to software, applications, or toolkits that create meshes in biological systems. - - - A measurement (or image acquisition) device that visualizes detailed internal structure and limited function of the body, using a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body. - MRI Scanner - pending final vetting: location in hierarchy and harmonize with OBI/eagle-i - - - - - - - - - - - - Averaging and Agglomeration - Resource that provides access to software, applications, or toolkits that performs signal processing by repeated measures of the signal and then calculates the expected value of the data set. - - - Activity - Activity of interest that may be related to a BRO:Resource. - - - Resource that provides access to software, applications, or toolkits that search, sort, or index on binary or textual formatted data. - - - - Searching Sorting and Indexing - - - Pressure Regulator - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - Network model - Deprecated for BRO v2.7 - - - - - - - - - - Reagent Resource - A material resource that provides access to reagents, such as antibodies or drugs. Included in this definition are sites designed to work with individual service providers of reagents such as ExactAntigen who do not sell antibodies directly, but provide a catalog with pricing information for most commercial and noncommercial antibody providers. Note, reagents may be of organismal origin or not, but must be classified as macromolecules or molecules. - - - - - - - Data Exploration - Resource that provides access to a visualization tool that is able to display data as an image or graphical representation. - - - Narrative Resource - A resource that provides a literary work, book, story, textual description, or account of events, experiences, or the like, whether true or fictitious. - - - - Work with NIF to define blog and wiki. - - - Data Analysis Software - A resource that provides access to software or application that is used to analyze, model, and transform data with the goal of testing a research hypothesis, highlighting useful information, suggesting conclusions, or supporting decision making. - - - - - - - - - Resource that provides access to software, applications, or toolkits that can be used to calculate the estimate of side chains of conformations in biomolecular configurations. - Prediction of Side-Chain Conformations - - - A microscope (device to magnify small objects) in which objects are lit directly by white light. - Light Microscope - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - Resource that provides access to software, applications, or toolkit that analyze biological graphs. - Graph Analysis - - - - - - Metabolomics Facility - pending final vetting: Refine definition - - - - A molecular biology facility devoted to metabolomics (http://en.wikipedia.org/wiki/Metabolomics) - - - Symbolic and Analytic Model - Resource that provides access to methods of analysis and modeling that have closed-form analytical mathematical representations. - - - - - - Data Normalization - Resource that provides access to software, applications, or toolkits that reduces systematic sources of variation from data. - - - - - - Federal Funding Resource - A funding resource where money is obtained from the central government. - - - - - - - - - Deprecated for BRO v2.7 - Material supplies provided for research (http://en.wikipedia.org/wiki/Research) purposes - - - Research Supplies - - - Outlier Detection and Removal - Resource that provides access to software, applications, or toolkits that perform quality assurance on data to detect and/or remove outliers. - - - - - - Epidemiology - As defined in http://en.wikipedia.org/wiki/Epidemiolgy - - - - - - Disaster Recovery Service - - A resource that provides the ability to retrieve archived content in the event of a disaster that impacts the system in question. - - - A resource that provides any kind written item, as a book, article, or letter, esp. of a factual or informative nature. - - - - - - - - Document - Deprecated for BRO v3.0 - - - A facility or core devoted to localizing antigens (eg. proteins) in cells of a tissue section through antibodies binding specifically to antigens. - Immunohistochemistry Facility - - - - - - Deep Parsing - - - - Resource that provides access to applications, libraries, or software that detect relationships between language constructs. - - - - - - General (hyper)volume visualization tools (e.g., volume rendering). - - Manifold Viewers - - Deprecated for BRO v2.7 - - - As defined in http://en.wikipedia.org/wiki/Physiology - - - - Physiology - - - - Data Service - A resource that provides data management and specialized use. - pending final vetting: review location in hierarchy - - - A resource or expertise relating to psychometrics (http://en.wikipedia.org/wiki/Psychometrics) - Psychometrics Expertise - - - - pending final vetting: refine definition - - - A license that grants the right of usage from a third party distributor to the end user. - Deprecated for BRO v3.0 - - - - Pass Through License - - - - - - - As defined in http://dictionary.reference.com/browse/facility - Facility Core - A resource that provides instruments, technologies, facilities, and/or expert support for a specific area of research. - pending final vetting: suggest to re-name to Core Facility, discuss how to manage change. - - - - - - - - - - - - Deprecated for BRO v2.7 - - - - - Scripting Language and Environment - - - - Resource that provides access to software, applications, or toolkits that perform image pre-processing routines that are required as preliminary steps before standard image processing, analysis and visualization take place. - - - - Pre-Processing - - - Data distribution that does not have a data model or has one that is not easily usable by a computer program. - - Deprecated for BRO v3.0 - - - - Unstructured Data - - - - - - - - - Language Summarization - Resource that provides access to applications, libraries, or software that creates a shortened version of text. - - - As per alignment with NIF resource type hierarchy. - - Resource that provides access usually through repositories or the Internet to computer executables, libraries, plugins, or source code. - Software - - - A resource that provides access to the ability to generate antibodies that bind to a specific antigen. - Antibody Production - - - - - - - - - Software Development Tool - Resource that provides access to software, application, or toolkit that enable generic tools for software development, engineering and deployment. - - - Deprecated Resource - Former subclasses of BRO:Resource that have been deprecated and their usage is not recommended. - - - - Discrete data that contains many variables. - High Dimensional Data - - - - - - Deprecated for BRO v3.0 - - - Microtome - An instrument used to cut very fine sections of material. - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - pending final vetting: review definition - Resource that provides access to software, applications, or toolkits that calculate the time course of biomolecular configurations and their classification. - - Molecular Modeling and Classification - - - Deprecated for BRO v3.0 - - - Connectivity Matrix - - - - A matrix is a subset of a network that contains node-edge-node connections of interest and are represented as a matrix. - - - - - - A resource that provides services to ensure research is conducted in accordance with environmental and safety standards (e.g. laboratory safety procedures, radiation safety procedures, disposal protocols, etc). - Environmental Health and Safety Resource - - - - Deprecated for BRO v3.0 - Summarization - - - Resource that provides access to applications, libraries, or software that creates a shortened version of text. - - - - An educational resource that is interactive and teaches by example. - Tutorial - - - A resource that provides data related to any kind of measurement designed to describe an observable characteristic or trait. - Phenotypic Measurement - - - - - - Parsing - - - - Resource that provides access to applications, libraries, or software that analyze text to detect language constructs or tokens such as noun phrases and verbs. - - - A resource that provides clinical care data at the level of an individual. - - - - Individual Human Data - - - Area of Research - Area of research that may be related to a BRO:Resource. - - - - - - Pharmacokinetics Pharmacodynamics Expertise - pending final vetting: refine definition - A resource or expertise relating to pharmacokinetics (http://en.wikipedia.org/wiki/Pharmacokinetics) and pharmacodynamics (http://en.wikipedia.org/wiki/Pharmacodynamics) - - - - - - A resource that provides space for and access to a database. - Database Hosting - - - - Graphical Composition - Resource that provides access to software, application, or toolkit that enable graphical composition of applications. - - - - - - - pending final vetting: propose definition - Computational Hosting - - - - - - - - Discrete data that is composed of individual data points as compared to. - Deprecated for BRO v3.0 - Scalar Data - - - - - - A resource that provides image data consisting of length and width, but no depth. - Two D Image - - - - Compiler - A resource that provides a computer program (or set of programs) that transforms source code written in a computer language (the source language) into another computer language (the target language, often having a binary form known as object code). The most common reason for wanting to transform source code is to create an executable program. A \\u201ccompiler\\u201d is primarily used for programs that translate source code from a high-level programming language to a lower level language (e.g., assembly language or machine language), and is likely to perform many or all of the following operations: lexical analysis, pre-processing, parsing, semantic analysis, code generation, and code optimization. - - - - Named Entity Recognition - Resource that provides access to applications, libraries, or software that attempts to identify and classify atomic elements in text into predefined categories such as the organizations, locations, expressions of times, quantities, and names of people. - - - A resource that provides data storage and maintenance, such as a database that accepts submissions of similar data for storage and use. For example, the cell centered database (CCDB) encourages submissions of anatomical images that will increase its' holdings. - Data Storage Service - - - - - - Statistical Text Analysis - - Resource that provides access to software, applications, or toolkits that performs statistical tests on text corpora. - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - A neurosurgical device that supplies a controlled alternating-current voltage to two electrodes that are applied to a patient. - - - - Stimulator - - - Wavelet Transform - Resource that provides access to software, applications, or toolkits that performs multi-dimensional wavelet transform. - - - - - - - - - A molecular biology facility devoted to the study of genomics (http://en.wikipedia.org/wiki/Genomics) - Genomics Facility - pending final vetting: Refine definition - - - - - - - - A resource that provides access to data from individual experiments. - Deprecated for BRO v3.0 - Experimental Measurement - - - - - - pending final vetting: Refine definition - A facility or core devoted to developing animal research models (http://en.wikipedia.org/wiki/Animal_models) - Animal Models Facility - - - - - - Root Finder - A resource that provides access to a tool or function that finds a value x such that f(x) = 0, for a given function f. Such an x is called a root of the function f. - - - - - - Continuum Method Simulation - Resource that provides access to software, applications, or toolkits that uses all data points in a simulation. - - - Resource Description - - - - - - - Seminar Series - A resource that provides presentations from experts within their field. - - - Framework solutions that enable scientists to work smarter and ultimately increase the number of scientific discoveries made, as well as decrease the time to publish results. (http://en.wikipedia.org/wiki/Information_technology) - Research IT - - - - Biospecimen Management - Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository) - - - - Named Entity Normalization - - Resource that provides access to applications, libraries, or software that map the recognized entities to unambiguous references to real world entities. - - - pending final vetting: review location in hierarchy - Document Retrieval - - Resource that provides access to software, applications, or toolkits that provides an electronic document or file in response to a query. - - - - Server - Deprecated for BRO v3.0 - A resource that provides any combination of hardware or software designed to provide services to clients as defined in http://en.wikipedia.org/wiki/Server_(computing) - - - - - Protein Interaction Modeling - Resource that provides access to software, applications, or toolkits that can be used to model protein interactions. - - - - - - - - - A molecular biology facility devoted to PCR (http://en.wikipedia.org/wiki/PCR) - pending final vetting: Refine definition - PCR Facility - - - pending final vetting: refine definition - - - - Grant Preparation Expertise - A resource or expertise relating to grant preparation (http://en.wikipedia.org/wiki/Grant_(money)) - - - Standalone Application - - Deprecated for BRO v3.0 - - - - - Resource that provides access to software distribution that does not have any dependencies. Software distributed in this manner can be run on a desktop computer. - - - - Social Networking - As defined in http://en.wikipedia.org/wiki/Social_network - - - A resource that provides guidelines and information related to research involving humans with the aim to protect the rights and welfare of research subjects. Such resources could supply consent forms, patient questionnaires, assist in ethical protocol designs, host seminars on conducting human studies, etc. - Human Studies Compliance Resource - - - - - - Computer-Instrumentation Interface - pending final vetting: work with eagle-i to define terms since out of scope of BRO - A part of an instrument that provides for human user input to operate the instrument. - - - - - - - Hosting - A resource that provides a server for data or programs that another computer can access by means of a network. - - - A resource that provides calculating or processing over a data input, such as interpreting EEG data. Note, this may include human and/or computer expertise, so that a software tool may be included as a data computation service. - - Data Computation Service - - - A resource that provides access to tools or function that are used to reconstruct 2D and 3D images based on projections of an object. - Image Reconstruction - - - - - - Biomolecular Interaction Facility - - - - A molecular biology facility devoted to the study of interactions between molecules in biology. - pending final vetting: Refine definition - - - Clinical Studies - or resources that help investigators do clinical studies or trials, including, epidemiology (http://en.wikipedia.org/wiki/Epidemiology), outcome development, physiological human studies, interventional trials, etc - - - - - - - Resource that provides access to software, applications, or toolkits that searches documents for information within the document and metadata about the document. - Information Retrieval - - - A resource that provides aid or assistance with a technology product. - Technical Support - - - - - - - pending final vetting: refine definition - - - A measurement (or image acquisition) device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting -radionuclide (tracer), which is introduced into the body on a biologically active molecule. - pending final vetting: location in hierarchy and harmonize with OBI/eagle-i - PET Scanner - - - - - - - - - Biositemaps Information Model - - - Reagent Manufacture - A resource that manufactures a product that could have a role as reagent. Examples include producing antibodies to a particular antigen (Charles River custom antibody service) or designing drugs which fit a receptor. - - - - - - - Deprecated for BRO v3.0 - Resource that provides access to software, application, or toolkit that can develop access to a connected group of pages on the World Wide Web regarded as a single entity, usually maintained by one person or organization and devoted to a single topic or several closely related topics. - Website - - - - - - Resource Integration Component - Resource that provides access to software, application, or toolkit that enable integration of diverse resources. - - - - - - Shape Analysis - Resource that provides access to tools representation, modeling, analysis and visualization of biological shape out of data. - - - An instrument that increases the output of another instrument. - pending final vetting: work with eagle-i to define terms since out of scope of BRO - Amplifier - - - - - - - - - Proposed children: -- Bayesian network -- Correlation network -- Pathway network -- Causality network - -e.g. Sage Bionetworks will be publishing exactly these types of models. - A resource that provides access to a computational model representing objects and their relationships. - Network Model - - - - A resource the provides access to a publicly available document that is generated by a governing entity. - Government Publication - - - Deprecated for BRO v3.0 - Modular Component - Resource that provides access to a software component. - - - - - - - - Proteomics Facility - - - - A molecular biology facility devoted to proteomics (http://en.wikipedia.org/wiki/Proteomics) - pending final vetting: Refine definition - - - Animal Care Facility - - - - A facility or core devoted to the care of research animals. - pending final vetting: Refine definition - - - Deprecated for BRO v3.0 - - Deprecate - - - - Network Editor - - - - Integration and Interoperability Tools - - - - - - These are resources that allow tool interoperability and resource integration and data mediation. - Deprecated for BRO v2.7 - - - - - - The dimensions of the array in computer memory used to store the data acquired during a pulse sequence. Related to the number of phase-encoding steps, frequency-encoding points and number of slices. - Deprecated for BRO v3.0 - Matrix - - - - - A resource that provides access to tools or functions that model biological processes that involves random sampling in the algorithm. - Monte Carlo Simulation - - - - - - Regulatory Compliance - As defined in http://en.wikipedia.org/wiki/Regulatory_compliance - - - - Calendar Schedule and Resource Management - A resource that provides functionality to allocate resources based on a method of timekeeping. - - - - Immune Monitoring Facility - A facility or core devoted to assessing effects on the human immune system (immunogenicity, immunocompetence, immune reconstitution, immunotoxicity, and immunopathology) of particular importance in the study of disease and therapeutics. - - - - - - A resource that provides the entire environment (applications, servers, network) that provides comprehensive facilities to computer programmers for software development. An SDE typically includes an integrated development environment (IDE, comprising source code editor, compiler, build automation, debugger), requirement management tools, design modeling tools, documentation generation tools, code analysis tools, and so on. - Software Development Environment - - - - - - - Graph Alignment - Resource that provides access to a graph algorithm that compares the similarity of graphs to each other. - - - Resource that provides access to software or application that perform numerical analysis or other canonical computational methods that act either on experimental or synthetic data. - Algorithm - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - Microarray Scanner - An instrument which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip. - - - Resource that provides access to software, applications, or toolkits that model or simulate interaction between biological components such as genes, proteins, cells, organs, populations. - Interaction Modeling - - - - - - - Inhomogeneity Correction - Resource that provides access to software, applications, or toolkits that performs methods for correction of image intensities where non-biological and non-physiological drift or noise is introduced by the scanning hardware. - - - Statistical Package - - - - A resource that provides access to self-contained tools, resources and packages for statistical modeling and data analysis (e.g., R, SOCR, SAS, SPSS, SYSTAT, etc.). - - - Statistical Analysis - - A resource that provides access to software, applications, or toolkits for basic statistical modeling and analysis. - - - - Provenance - Deprecated for BRO v2.7 - - - - - - physico chemical models - - - - - Deprecated for BRO v2.7 - - - - - - - - A resource that provides the manufacture of a piece of hardware. An example is producing a made to order microarray chip. - Instrument Manufacture - - - - - - Resource that provides access to an ontology and development management tool that identifies differences between two ontologies. - Ontology Diff and Alignment - - - The study of all the genes of a cell, tissue, or organism at the DNA (genotype) or mRNA (transcriptome) levels. - Genomics - - - - Resource that provides access to software, application, or toolkit that enables software or application integration using graphical methods. - - - - Graphical Integration - - - Ontology - A resource that provides access to a set of concepts within a domain and the relationships between those concepts, used to reason about the objects within that domain. - - - - - - - - - Pattern Inference Algorithm - A resource that provides access to tools or functions that derive reduced significant information about experimental or synthetic data. - - - Resource that provides access to software, application, or toolkit that enables an interactive software development tool that runs on different computer operating systems. - - Cross-Platform Tool - - - - Deprecated Data Resource - Created in BRO v2.7 - Former subclasses of BRO:Data_Resource that have been deprecated and their usage is not recommended. - - - - As defined in http://en.wikipedia.org/wiki/Pediatrics - - Pediatrics - - - - A resource that provides a software environment created to investigate the quality of the product or service under test, with respect to the context in which it is intended to operate. This includes, but is not limited to, the process of executing a program or application with the intent of finding software bugs. - Code Testing Framework - - - Homology Modeling - Resource that provides access to software, applications, or toolkits that uses a proteins amino acid sequence and an experimental three-dimensional structure of a related homologous protein to generate an atomic-resolution model of the protein. - - - - - Pharmacokinetics Pharmacodynamics - As defined in http://en.wikipedia.org/wiki/Pharmacokinetics and http://en.wikipedia.org/wiki/Pharmacodynamics - - - Resource that provides access to software, applications, or toolkits that can be used model a system using or described by wavelets. - - - - Wavelet Model - - - Bibliographic Resource - A resource that contains information about or access to published sources. - - - - - - - - - - Registration - Resource that provides access to software, applications, or toolkits that performs methods for co-registration, alignment and warping of imaging and hyper-imaging data. - - - Resource that provides access to software, application, or toolkit that is able to alter information. - Data Editor - - - - Information Resource - A resource that provides data, knowledge or narrative. - As per alignment with NIF resource type hierarchy. - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - An instrument for measuring alternating or varying electric current in terms of current and voltage. - Oscillograph - - - Object Database - - A resource that provides access to a database that represents information in the form of objects. - - - Resource that provides access to software, applications, or toolkits that perform spatial and frequency-type data transformations. - - Spectral Transform - - - Resource that provides access to Community and User Interaction Systems, educational resources and web-services. - Dissemination Vehicle - - - - - - Data Transforms - - Deprecated for BRO v2.7 - - General data transformations - - - - Interactive Network Analysis - - Resource that provides access to software, application, or toolkit that analyze networks interactively with a user. - - - Resource that provides access to software, applications, or toolkits that model the processes of a cell. - - - - Cell Model - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - Microscope - An instrument used to obtain a magnified image of small objects and reveal details of structure not otherwise distinguishable. - - - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - Electrode Holder - - - - An instrument that provides a means of coupling fluid-filled glass microelectrodes to a patch clamp amplifier for the measurement of electrical currents or potentials. Holders are available in straight angle configurations made out of polycarbonate or Teflon, and usually feature a silver/ silver chloride pellet attached to a BNC-compatible pin/ending. A suction port is standard for holders meant for patch clamp recordings, but are not included in holders meant for sharp electrode recordings or extracellular recordings. - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - Power Conditioning Unit - - - - - - Resource that provides access to software, application, or toolkit that has mechanisms for sharing information between members of a group working on a shared project. - - Communication and Collaborative Work - - - Resource that provides access to methods of analysis or generation of networks and graph data structures. - Graph Algorithm - - - - - Deprecated Activity - Former subclasses of activity:Activity that have been deprecated and their usage is not recommended. - - - Sequence Similarity Searching - Resource that provides access to tools or functions that perform similarity searching involving biological sequences. - - - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An instrument to place and store other instruments. - - - - Rack - - - Molecular and Cellular Data - - - - A resource that provides data related to molecular and cellular properties and their relationship to macroscopic parameters. - - - Micromanipulator - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An instrument that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. - - - - - - A resource that provides a service the output of which is a material object. That material object might be an instrument, a chemical, or an animal. - Material Service - - - - - - Resource that provides access to software, applications, or toolkits that involves atoms and molecules are allowed to interact for a period of time by approximations of known physics. - - Molecular Dynamics - - - - - - Numerical Integrator - Resource that provides access to tools or functions that calculate the numerical value of a definite integral. - - - A resource that provides access to a database that comprises a normalized data set constructed according to a specific entity-relation data model. - Relational Database - - - - Online Support - Resource that provides access to software, application, or toolkit that enable help via internet accessible material. - - - - - - - - Deprecated for BRO v2.7 - Numerical Integrators - - - - - - Knowledge Extraction - - Resource that provides access to software, applications, or toolkits that recognize and report on entities and relations in text corpora. - - - - - - Resource that provides access to software, applications, or toolkits that model or simulate biological processes using computational meshes. - Mesh Model - - - - - Resource that provides access to software, applications, or toolkits that analysis multi-dimensional spatio-temporal data. - Signal Processing - - - - - - Resource that provides access to software, applications, or toolkits that can be used to model physiological processes of the cardiovascular system. - Cardiovascular Model - - - Deprecated for BRO v3.0 - - - - - Resource that provides access to software, applications, or toolkits that performs exploratory data analysis methods. - - EDA - - - Resource that provides access to software, applications, or toolkits that can be used to visualize a configuration of biomolecules in space and time. - - Molecular Visualization - - - Software Technology Protocol - - A resource that provides access to information on how to implement and use a computer program. - - - - - - A resource or expertise in research (http://en.wikipedia.org/wiki/Protocol_(natural_sciences)) or clinical-trial protocol (http://en.wikipedia.org/wiki/Clinical_trial_protocol) - Protocol Development Expertise - pending final vetting: refine definition - - - Data Acquisition Software - - Resource that provides access to software or application that support collection of real-world conditions and converts these to a numerical representation that can be processed by a computer, http://en.wikipedia.org/wiki/Data_acquisition. - pending final vetting: review term in comparison to siblings data analysis software and data processing software - - - - pending final vetting: provide definition - - - - Volume Model Scene Data - - - - - - A resource that provides access to structured data that is in XML, a self-descriptive format to store and transport data. - XML Data - - - Resource that provides access to software, applications, or toolkits that can be used to classify protein shape and parameters. - - Structure-Based Protein Classification - - - A resource that provides access to reports that are published journals - - Journal Article - - - Resource that provides access to software, applications, or toolkits that enable integration and interoperability tools that facilitate communication between software tools via graphical workflow pipelines. - pending final vetting: review definition - Graphical Processing Workflow Environments - - - - - - Resource that provides access to software, applications, or toolkits that perform alter the spatial-temporal spectral content of data. - Filtering - - - - - - - Numerical Model - Resource that provides access to software, applications, or toolkits that generate solutions from a numerical model. - - - - - - Resource that provides access to software, applications, or toolkits that can be used to provide quantitative data on the molecules being analyzed such as molecular weight, abundance or purity. - Analysis of Gel-Electrophoresis - - - - Tag as a resource for a specific Institutional Review Board (http://en.wikipedia.org/wiki/Institutional_Review_Board) - IRB - - - Data Resource - - A resource that provides individual facts, statistics or items of information. - - - - - - Mechanical Simulation - Resource that provides access to software, applications, or toolkits that model mechanical forces. - - - - White Paper - A publication that is an authoritative report or guide that often addresses issues and how to solve them. - - - A resource that provides items such as reagents, instruments, tissue samples or organisms for use in a laboratory. - Laboratory Supply Resource - - - - - - pending final vetting: Refine definition - Radioisotopes Facility - - - - A molecular biology facility devoted to radioisotopes or radionuclides (http://en.wikipedia.org/wiki/Radioisotopes) - - - - - - Resource that provides access to software, applications, or toolkits that calculate solutions to physiological processes that involve chemical kinetics, compartments, or stochastic interactions. - Physico-Chemical Model - - - - - - Intellectual Property Resource - A resource that provides legal counsel regarding contracts and agreements between an institution and various external parties. These resources may provide legal seminars along with training materials regarding intellectual property. - - - A resource that provides image data consisting of length, width and depth. - Three D Image - - - - - - A measurement (or image acquisition) device that generates a three-dimensional image of the inside of an object from a series of two-dimensional X-ray images taken around a single axis of rotation. - pending final vetting: location in hierarchy and harmonize with OBI/eagle-i - CT Scanner - - - - - - - - - - - - pending final vetting: review location in hierarchy - Image Processing - Resource that provides access to software, applications, or toolkits that performs image post processing (i.e., excludes image generation). - - - A resource that provides access to physical materials like tissue samples or organisms. For example, the IMSR enables acquisition of a transgenic mouse or cell line. Note, for the sake of simplicity we have excluded molecules of organismal origin from this category as these can be manufactured chemically and have included them under the reagent category (eg. antibodies, toxins). - - - - Biomaterial Supply Resource - - - A facility or core devoted to the act or practice of opening a vein by incision or puncture to remove blood. - - - - Phlebotomy Facility - - - A resource that provides monetary support in the form of grants, contracts, or gifts for research, training, or education. - pending final vetting: are more subclasses needed, e.g. Foreign_Funding_Resource and Local_Funding_Resource - Funding Resource - - As per alignment with NIF resource type hierarchy. - - - - - - - Numerical Methods - Deprecated for BRO v2.7 - General numerical modeling and computational tools (ala, GAMS: http://gams.nist.gov/) - - - - A resource that provides a simplified or symbolic representation representing the states of a system or network over time. - - - - Dynamic Model - - - Segmentation - - Resource that provides access to software, applications, or toolkits that classify sub-regions of images. - - - pending final vetting: refine definition - Cloud computing - - Integrated Hosting - - - - Interactive Tools - Deprecated for BRO v2.7 - - - - - Clinical Research Data - A resource that provides data on clinical trials and outcomes studies. - - - - Resource that provides access to software, applications, or toolkits that calculates mass spectra sequence and related data from experimental mass spectra data. - Mass Spectra Identification - - - - Community Structure Analysis - - Resource that provides access to a graph algorithm that identifies densely interlinked nodes in the graph. - - - Instrument - - - - pending final vetting: review scope of BRO for child terms - A resource that provides scientific instruments such as microscopes, amplifiers or dissection tools. For example, Grass Instruments is a site that sells amplifiers and other equipment useful for electrophysiology. From NIFSTD - - - An instrument to heat or cool an environment. - Temperature Control Unit - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - - Vibrotome - - An instrument for sectioning tissue samples that uses a vibrating razor blade to cut the sample. - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - - Electrode Puller - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - An instrument to make micropipettes. - - - A resource that provides data related to the measurement of interaction between molecules of any type. - Molecular Interaction - - - - Cross-Language Wrapping - Resource that provides access to software, application, or toolkit that enables an interactive software development tool that creates language bindings. - - - - Hyperbolic Graph - Resource that provides access to hyperbolic space (hierarchical) graph/tree visualization tools. - - - - Resource that provides access to software, applications, or toolkits that is used to model or simulate biological structures, kinetics, function, structure, random events, and genotype or phenotype in time and space. - Modeling and Simulation - - - - Resource that provides access to software, applications, or toolkits that allows insertions, deletions, or mismatches in nodes/edges. - Approximate Graph Alignment - - - - - Research Funding - - Activity related to learning about, securing, and managing money to support research - - - - - - Gene Therapy - As defined in http://en.wikipedia.org/wiki/Gene_therapy - - - Tutorials - - - - - Deprecated for BRO v2.7 - - - - - - - - Portal - pending final vetting: review NIF hierarchy for source of children terms. - A Resource that provides a point of access to information on the World Wide Web, presenting information from diverse sources in a unified way. - - - Activity related to gathering and inventory of resources, e.g., biositemaps - Resource Inventory - - - - - A resource that provides data from any material sample that was given to the service provider. This can also be a service which performs an experiment such as electrophysiological examination of LTP magnitude in the presence of a drug given to the service provider. Viewing this as an input/output relationship the input would involve a drug and the output would be data such as a dose response curve. - Material Analysis Service - - - - Outcomes Research - As defined in http://en.wikipedia.org/wiki/Outcomes_research - - - - - - A resource that provides access through the Internet or archive to formatted digital or textual data. - Data Storage Repository - Deprecated for BRO v3.0 - - - - - - Resource that provides access to software, application, or toolkit that enables a software development tool that combines software documentation with generating source code. - Integration - - - - - - A facility that provides resources for the development and growth of self-renewing cells that are capable of differentiation into a diverse range of specialized cells. - Stem Cell Therapy Facility - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An automated mechanical machine for creating microarrays - - Robotic Arrayer - - - - - - A facility or core for generating recombinant vectors containing a functioning copy of a human gene. - Gene Therapy Facility - - - Structured Knowledge Resource - - A resource that provides access to collection of data records arranged according to some semantic framework. The semantic framework may be minimally expressive - such as a simple controlled vocabulary - or highly expressive such as a formally structured ontology. Such resources may include only a representation of universal/classes/categories or may be linked to individual instance data typed according to a set of asserted classes (i.e., a knowledgebase). - - - Regulatory Signaling Network Reconstruction - - - - PML Resource that provides access to tools or functions that generate network maps of biological signaling or regulatory networks based on applying logic and statistics to observations/hypothesis. - - - pending final vetting: Refine definition - A molecular biology facility devoted to monoclonal antibody (http://en.wikipedia.org/wiki/Monoclonal_antibody) research and uses. - Monoclonal Antibody Facility - - - - - - - - Deprecated for BRO v2.7 - thing stores data - - - Data Storage - - - Stochastic Data - - - - - Deprecated for BRO v3.0 - - - Resource that provides access to software, applications, or toolkits that calculate molecular forces in a biomolecular system. - Molecular Force Field Calculator - - - - - - Deprecated for BRO v3.0 - Source Code - - Resource that provides access to information content entity that specifies, using a programming language, some algorithm. - - - As defined in http://en.wikipedia.org/wiki/Bioinformatics - Bioinformatics - - - - Mass Spectrometer - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. - - - A resource that provides material storage, maintenance and retrieval, such as the Harvard brain tissue bank. - - - - Material Storage Service - - - Sentence Splitting - - Resource that provides access to applications, libraries, or software that divide sentences into components or fragments. - - - - - - Human Embryonic Stem Cell Resource - A resource that provides guidance and information regarding the use of embryos or human embryonic stem cells in research. - - - - As defined in http://en.wikipedia.org/wiki/Health_services_research - Health Services - - - A resource that provides data that is partially structured. - Semi-Structured Knowledge Resource - - - - - - - Resource that provides access to software, applications, or toolkits that manage software pipelines - Pipeline Manager - - - A resource that provides general education to the public. - Outreach Program - - - - - Source Control - Resource that provides access to software, application, or toolkit that enable software source control methods. - - - Optimizer - - - - A resource that provides access to a tool or function that locates the extremum (usually minimum) of a cost function subject to constraints., - - - A resource that provides access to a communication between an agent and one or more specific recipients., - Personal Communication - - - - Network Characterization - - - - Resource that provides access to tools or functions that describe a connectivity between components at the genomic, molecular, cellular, tissue level, or population levels. - - - - Interactive Web-Based Tool - Resource that provides access to software, application, or toolkit that enables hands-on resources for data management (entry, query, traversal, comparison, etc.) - - - - Resource that provides access to software, applications, or toolkits that smooths time series data. - Regularization and Smoothing - - - A resource that provides training to people. - Training Service - pending final vetting: review location in hierarchy - - - - - - Microscopy Facility - A facility that provides microscopes with which to view samples or objects. - - - - - - Resource the provides access to tools or functions that implements the canonical convolution or operation that describes the action of a linear system on a signal. - Convolution - - - - - - - - - - - - A physiology facility devoted to neurology (http://en.wikipedia.org/wiki/Neurology) research - pending final vetting: Refine definition - Neurological Facility - - - - Gene Expression - A resource that provides data on the abundance of RNA that is coded from genes. - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An instrument used to perform NMR of a sample. - NMR Instrument - - - Authorization - - - - The process of specifying access rights to a resource. - - - - Chamber - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An instrument that forms an enclosed space. - - - - - - A resource that provides access to scientific data assessment instruments, for example behavioral assessment tests. - Assessment Material Resource - - - Behavioral Science - As defined in http://en.wikipedia.org/wiki/Behavioral_science - - - - - A resource that provides items such as reagents, instruments, tissue samples or organisms. - Material Resource - As per alignment with NIF resource type hierarchy. - - - - - Free Text - - Deprecated for BRO v3.0 - Unstructured data in a format of alphanumeric characters. - - - Fourier Transform - - Resource that provides access to software, applications, or toolkits that performs Multi-dimensional Fourier transform - - - - - - Resource that provides access an interactive software tool that enables tagging data with ontology terms. - Data Annotation - - - - A resource that provides access to a generally agreed upon set of rules for representation. - Standard Specification - - - Deprecated for BRO v3.0 - - - - A data object that consists of separate, but finite set of values. - Discrete Data - - - Innovative therapeutics (http://en.wiktionary.org/wiki/therapeutics) - Therapeutics - - - - Data Transfer and Communication - A resource that provides access to software or application that is used to transmit formatted textual or binary data. - - - - Small Molecule - - As defined in http://en.wikipedia.org/wiki/Small_molecule - - - - - - A resource that develops policies and procedures related to associations between academia and industry to ensure that the advantages of these connections are not being achieved at the expense of the fundamental values of objectivity in research. - Conflict of Interest Resource - - - A Resource that provides access to a graph algorithm that uses ranking of network elements to identify the importance of elements in a network. - Centrality Analysis - - - - License and Terms for Redistribution - - A license that describes the constraints for sharing the resource. - Deprecated for BRO v3.0 - - - - - - - - Discrete data that consists of x, y, and z coordinates. - Deprecated for BRO v3.0 - Three Dimensional Data - - - - - Statistical Algorithm - - Resource that provides access to tools or functions that calculate basic methods of statistics and biometrics. - - - - pending final vetting: Refine definition - Physiology Facility - A facility or core devoted to physiology (http://en.wikipedia.org/wiki/Physiology) - - - Industry Partnership Expertise - - - - Expertise for liaison with Industry (http://en.wikipedia.org/wiki/Industry) - pending final vetting: refine definition - - - Aggregate Human Data - - - - A resource that provides data from clinical care that comprises combined data from multiple individual human subjects. - - - Image - pending final vetting: review location in hierarchy - A resource that provides data in the form of images. - - - - - - Novel Therapeutics - Deprecated for BRO v2.7 - Innovative therapeutics (http://en.wiktionary.org/wiki/therapeutics) - - - - - - A resource that provides access to software or application that is used to enable (i) interoperability and association of data and/or (ii) pipeline of online tools. - Integration and Interoperability Tool - - - - - As defined in http://en.wikipedia.org/wiki/Community_engagement - Community Engagement - - - Resource that provides access to software, applications, or toolkits that can be used to specifically model protein structure and function. - Protein Model - - - - Partial Parsing - Resource that provides access to applications, libraries, or software that parse part of a text or corpus. - - - - - Knowledge Environment - Deprecated for BRO v3.0 - - A resource that provides access to collaborative knowledge building, decision making, inference or discovery tools. - - - - - A funding resource that is provided by a state. - State Funding Resource - - - The process of confirming the correctness of the claimed identity. - - - - Authentication - - - Resource that provides access to a ontology development and management tool that is used to generate an image of the ontology. - Ontology Visualization - - - - - - Application Programming Interface - - Resource that provides access to software, application, or toolkit that enables or can be used to develop application programming interfaces. - - - Atlas Generation - Resource that provides access to software, applications, or toolkits that generate computational atlases of biological objects using imaging techniques. - - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - Oscilloscope - An electronic measuring instrument that creates a visible two-dimensional graph, on a screen, of one or more continuously varying voltages or currents. - - - - Private Funding Resource - A funding resource where money is supplied by a non governmental organization, foundation, or company. - - - A resource that provides access to software or application that is used to convert or manipulate data into information or knowledge. - - Data Processing Software - - - 3-D models evolving in time - Deprecated for BRO v3.0 - Four Dimensional Data - - - - - - - Resource that provides access to molecular sequence viewers. - Sequence Visualization - - - - - - A resource which can include a committee or a board that reviews research protocols and conducts evaluations of the animal care facilities. The resource can be used to ensure the use of animals in research follows the required legal and ethical guidelines. - Animal Compliance Resource - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - An enclosure, formed by conducting material or by a mesh of such material, that blocks out external static electric fields. - - Faraday Cage - - - A resource that provides access to software or application that is used to analyze and model biological processes at the genomic, molecular, cellular, tissue level, or population levels. - - - Genomic Phenotypic Analysis - - - - - - - Resource that provides access to an ontology development and management tool that can be accessed via the Web. - Web Access - - - A resource comprised of one or more individuals who have specific expertise and provide professional or expert advice. - As per alignment with NIF resource type hierarchy. - - I spent some time thinking about the distinction between People Resources and Services Resources. Then I spent some time thinking of what would be subclasses of people. Below is the list I came up with. However, it bares striking similarity to what we had envisioned for Related Activity or Area of Research. Looking over at NIF, they defined People Resource as "A resource that provides access to individual people based, for example, on expertise or affiliation" and do not have any child nodes. I think I've come around to the opinion that we should either adopt NIF's approach, or change from having the top level People Resource to Consulting Resource as a child of Service Resource. (then still tbd whether to have children of that- I think I'd vote for not.) Note that we're already not in complete alignment at the top level- NIF has "Job Resource". I look forward to discussion with the group. - -- grant prep  -- business development    -- industry partnership -- toxicology  -- funding discovery  -- legal counsel  -- intellectual property  -- IRB  -- community outreach  -- finance  -- regulatory compliance  -- minority health  -- study design    -- clinical trials   -- basic research -- Informatics -- Biostatistics -- epidemiology -- development - People Resource - - - - Bug Reporting - Resource that provides access to software, application, or toolkit that enable web-based tools that provide structure to indicate a problem or issue. Typically, bug reporting software provides a mechanism to indicate the severity of the problem and a contact person to review the issue. - - - Ontology Development - - - - Resource that provides access to ontology and development management tool that allows a user to develop a set of terms, and the hierarchial relationship between them as well as metadata about the terms. - - - Testing Tools - Resource that provides access to a software development tool to perform quality assurance of software. - - - - pending final vetting: Refine definition - A facility or core devoted to research animals (http://en.wikipedia.org/wiki/Animal_testing) - Research Animals Facility - - - - Calculation of Solvent Accessible Area - - Resource that provides access to software, applications, or toolkits that can be used to determine the surface area of a molecule such as DNA or protein. - - - Structural Model - Resource that provides access to software, applications, or toolkits that can be used to model based on a coordinate-based mathematical description of a collection of biological structures. - - - - A resource that provides guidance related to ethical or legal matters concerning scientific research. These resources provide both information regarding ethical/legal research matters as well as methods for developing, applying, assessing and reviewing regulations (i.e. compliance documents, procedures, consent forms, etc). These resources can include both materials and documentation along with expertise in the form of personnel. - - - - Regulatory Compliance Resource - - - - Medical Device - A resource that provides devices used for therapy, diagnosis or surgery. - - - - - - - Deprecated for BRO v3.0 - Data file resulting from natural language processing. - Automated Natural Language Output - - - - A facility or core that provides resources for the growth of cells. - - - - Cell Culture Facility - - - Website Hosting - A resource that provides space for and access to a web server and content. - - - - As per alignment with NIF resource type hierarchy. - A resource that provides an act of helpful activity, consisting of an organized system of apparatus, appliances, technology, personnel, etc. - - Service Resource - - - - Heath Services - Deprecated for BRO v2.7 - - As defined in http://en.wikipedia.org/wiki/Health_services_research - - - - Micro Dissection Facility - A facility or core devoted to cutting apart tissue on a very small scale such as at the level of individual cells. - - - - - - Deprecated for BRO v3.0 - A resource that provides a software system designed to support interoperable machine-to-machine interaction over a network. Web services are frequently Web APIs that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services. - - - - Web Service - - - Protein Expression - - A resource that provides data related to the presence and abundance of proteins from a cell or tissue sample. - - - - Hypothesis Testing Algorithm - Resource that provides access to tools or functions for testing statistical hypothesis against data. - - - - Ontology Development and Management - Resource that provides access to software development tool that can be used to build a set of terms and specify the relationship between the terms. - - - A resource that provides a combination of computational resources from multiple administrative domains, applied to a common task. - Grid Computing - - - - Feature Request - Resource that provides access to software, application, or toolkit that enable interactive web-based tool that has functionality to collect a request for new features for a specified tool. - - - - Resource that provides access to software, applications, or toolkits that can be used perform simulations using sampling and re-sampling methods for random events. - Random Number Simulation - - - - Resource that provides access to software, applications, or toolkits that can be used to calculate the electrostatic potential of biomolecular configurations. - Numerical Calculation of Electrostatic Potential - - - - As defined in http://en.wikipedia.org/wiki/Psychometrics - - Psychometrics - - - - Software Development - - - - - - - - - Resource that provides access to tools for computational geometric representation and analysis. - Computational Geometry - - - - A resource that provides a simplified or symbolic representation of a system or phenomenon. - Computational Model - - - Atlas - A resource that provides anatomical data represented by spatially indexed anatomical maps. - - - - Portlet Component - Resource that provides access to software portlet. - - - Deprecated for BRO v3.0 - - - - Deprecated for BRO v3.0 - Data Repository - - A resource that provides data storage and maintenance, such as a database which accepts submissions of similar data for storage and use. For example, the cell centered database (CCDB) encourages submissions of anatomical images that will increase its' holdings. - - - - - - - A resource that provides computational building blocks for complex data types, individual facts, statistics or items of information. - Data Object - Deprecated for BRO v3.0 - - - - A resource that provides the analysis of biological samples. An example is genotyping transgenic mice. - Pathology Laboratory Screening - - - - - Hierarchical Tree - Resource that provides access to viewers of directed, acyclic tree-structures. - - - - pending final vetting: Refine definition - A physiology facility devoted to research into metabolism (http://en.wikipedia.org/wiki/Metabolism) - Metabolism Facility - - - - - - Pattern and Motif Inference - Resource that provides access to software, applications, or toolkits that generate patterns or motifs based on applying logics and statistics to observations/hypothesis. - - - - Resource that provides access to software, application, or toolkit that enables a software development tool that is able to generate textual information when included in computer source code as specially formatted comments. - Document Generation - - - Phenotype Management - - Resource that provides access to applications, libraries, or software that perform inference and information retrieval on biological phenotype data. - pending final vetting: review location in hierarchy - - - - Deprecated for BRO v3.0 - - - Heterogeneous Funding Resource - - - - - As defined in http://en.wikipedia.org/wiki/Pathology - Pathology - - - - XML Database - A resource that provides access to a database that stores XML. - - - - Resource that provides access to software, application, or toolkit that enables a software development tool create documentation of software source code. - Documentation Generation - - - - - Deprecated for BRO v2.7 - Linear Algebra Tools - - - - Resource that provides access to methods basic numerical analysis or other canonical computational methods that act on 1, 2, 3 or 4 dimensional images. - Image Algorithm - - - - - - Deprecated for BRO v3.0 - Support - A resource that provides aid or assistance with a technology product. - - - - - Deprecated for BRO v3.0 - Nonhuman Data - - Clinical data that is not derived from a person. - - - - An unpublished document, which may also be submitted to a publisher for publication. - - Paper - - - Toxicology Expertise - A resource or expertise relating to (http://en.wikipedia.org/wiki/Toxicology) - pending final vetting: refine definition - - - - As defined in http://en.wikipedia.org/wiki/Metabolomics - - Metabolomics - - - - A facility that provides resources relating to tissues used in biomedical research. - Tissue Organ Facility - - - Time Series Analysis - - Resource that provides access to software, applications, or toolkits that includes methods for analyzing time series data in order to extract meaningful statistics and other characteristics of the data. - - - Clinical Chart - - - Deprecated for BRO v3.0 - **previously was called Clinical_Charts_eg_Demographics -we think this should be deleted - - - - - Clinical Care Data - A resource that provides any type of data obtained in the course of caring for humans outside of measurements obtained in clinical trials. - - - Knowledge Mining and Capturing - Resource that provides access to software, applications, or toolkits that are used to extract hidden patterns from data. - - - - - pending final vetting: review location in hierarchy and child terms - Data Mining and Inference - - - A resource that provides access to software, application, or toolkits that merge data with analysis tools with the goal of testing a research hypothesis, highlighting useful information, suggesting conclusions, or supporting decision making. - - - A resource that provides access to structured data that is separated by a sequence of one or more characters to mark the boundary between plain text or data streams. - Delimited Table - - - - - - - Resource that provides access to software, application, or toolkit that enables application integration using mapping. - Mapper - - - Physioloigcal Model - - Resource that provides access to software, applications, or toolkits that can be used model physiology. - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - PCR Instrument - An instrument based on the PCR method (http://en.wikipedia.org/wiki/PCR) - - - Backup Archive Service - - A resource that provides long-term storage for back-up copies of files. - - - License - A resource that provides access to documented permission to do something, either from a government or under a law or regulation. - - - - - A resource that provides software which maintains the identity of a software user with their software account. - Identity Management - - - Resource that provides access to software, applications, or toolkits that calculate solutions to models with closed form. - Model with Closed Form Solutions - pending final vetting: review location in hierarchy - - - - - - Regulatory Policy Resource - A resource that provides guidelines for complying with federal, state, and local regulations (e.g. research integrity office, research policy office, etc). The resource can provide seminars, documents, and other items regarding regulations. - - - - Preclinical - The stages of biomedical research which take place in model organisms and cell lines, prior to first-in-human application of a diagnostic or therapeutic intervention. - - - Software Development Resource - - Resource that provides access to software, application, or toolkit that enable interactive tools for generating a computer program. - - - A resource that provides access to software, applications, or toolkits that are used in the development of database management systems. - - Database Software - - - - Vector Data - - Discrete data that representents physical entities as XY coordinates. - - Deprecated for BRO v3.0 - - - Patent - - A resource that provides access to documents describing the exclusive right granted by a government to an inventor to manufacture, use, or sell an invention for a certain number of years. - - - A resource that provides access to collection of data or information that is not easily queryable without using metadata about the resource. - Unstructured Knowledge Resource - Suggested child terms: audio track, slide, and video per NIF. Work with NIF to generate definitions. - - - - Structured File - A resource that provides access to an electronic document having and manifesting a clearly defined structure or organization that allows it to be executed. - - - - - Certificate Program - A resource that provides a document that certifies completion of the program. - - - - A resource that provides access to an enclosed facility that takes specified precautions for containment of dangerous biological agents, as defined by http://en.wikipedia.org/wiki/Biosafety_level - Biosafety Level Facility - - - - - - - Fast Fourier Transform - Resource that provides access to tools or functions that compute the discrete Fourier transform (DFT) and its inverse. - - - - Feature Analysis - Resource that provides access to methods for automated analysis of object features and quantitative characterization of data. - - - - Experimental Protocol - A resource that provides detailed plans for a scientific experiments, medical trials, or other pieces of research. - - - - Natural Language Processing - A resource that provides access to software, library, or application that interprets human (natural) language into a machine-interpretable form. - - - Resource that provides access to software, application, or toolkit that enables professional software engineering processes. - Software Engineering Tool - - - - - Numerical Method - Resource that provides access to methods of numerical analysis or computational tools (ala, GAMS: http://gams.nist.gov/). - - - Continuing Medical Education - - A resource that provides post-grad education for physicians. - - - Resource that provides access to software, applications, or toolkits that methods for removing of segments from images, which have no valuable information about the biological object. For example, removing non-brain tissue from whole-brain MRI scans, for the purpose of doing quantitative evaluations of time or space changing brain anatomy. - Skull Stripping - - - - pending final vetting: Refine definition - NMR Facility - - - - A molecular biology facility devoted to NMR (http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance) research - - - A resource that produces a product that is of organismal origin. An example of a biomaterial service is the production of a knockout mouse or cell culture. Note, for simplicity of definitions all molecules including antibodies and toxins are considered reagents even though some may have an organismal origin. - Biomaterial Manufacture - - - - Resource that provides access to tools or functions that provide information beyond biological sequence, e.g., function. - - Sequence Annotation - - - Workbench - - - Resource that provides access to software, applications, or toolkits that can be used to build or manage frameworks that provides sets of interoperable software tools. - - - A facility or core for biomedical imaging. - - Imaging Facility - - - Biobank Facility - A facility or core that provides storage for any type of biospecimen. - - - - - - - Cell Processing Clean Room Facility - A resource that provides access to an enclosed environment that has a low and controlled level of environmental pollutants such as dust, airborne microbes, aerosol particles and chemical vapors. - - - - A resource that provides data or allows users to access and utilize data - Data Distribution - - Deprecated for BRO v3.0 - - - - Resource that provides access to software, applications, or toolkits, that generate a conclusion or finding based on applying logics and statistics to observations/hypothesis. - Inference From Data - - - - pending final vetting: work with eagle-i to define terms since out of scope of BRO - - A microscope that produces an electronically-magnified image of a specimen for detailed observation. - EM - Electron Microscope - - - - pending final vetting: Refine definition - Molecular Biology Facility - A facility or core devoted to molecular biology (http://en.wikipedia.org/wiki/Molecular_biology) - - - Deprecated for BRO v3.0 - - - A document that is publicly available. - Publication - - - - - A resource that provides tools or functions that aligns data with a model of the data. - Model Fitting Algorithm - - - - A resource that provides access to instruments, technologies, facilities, and/or expert support devoted to cell biology (http://en.wikipedia.org/wiki/Cell_biology) research - Cell Biology Facility - - - Former subclasses of area:Area_of_Research that have been deprecated and their usage is not recommended. - - Deprecated Area of Research - - - - A facility or core that provides services for research on sleep problems. - Sleep Study Facility - - - - Biomedical Supply Resource - Biomedical (http://en.wikipedia.org/wiki/Biomedicine) supplies provided for a laboratory (http://en.wikipedia.org/wiki/Laboratory) - pending final vetting: suggest to deprecate - - - Resource that provides access to software, applications, or toolkits that simulate the effect of contact between objects. For example an articular contact model to study articular surface stresses. - Contact Modeling - - - - Resource that provides access to software, applications, or toolkits that enable electronic communication. - - Communication Interface - - - - As defined in http://en.wikipedia.org/wiki/Training - Training - - - Behavioral Analysis Service - A resource that provides data from whole behaving animals, which are either provided to the service provider or purchased by the service provider specifically for the experiment which the provider was contracted to perform. Viewing this as an input/output relationship the input would be an animal and the output would be data such as an excel sheet of times of escape from the Morris water maze. - - pending final vetting: review hierarchy location - - - - Exploratory Data Analysis - Resource that provides access to software, applications, or toolkits that performs exploratory data analysis methods. - - - Mailing List - - Resource that provides access to software, application, or toolkit that enable interactive Web-based tool that can be used to send information to groups. - - - Version Source Control System - A resource that provides a system for the management of multiple revisions of the same unit of information. It is most commonly used in engineering and software development to manage ongoing development of digital documents like application source code, art resources such as blueprints or electronic models, and other projects that may be worked on by a team of people. - - - - Online Course - - Resource that provides online training and educational resources. - - - - As defined in http://en.wikipedia.org/wiki/Medical_device - Medical Device Development - - - - Cardiovascular Facility - pending final vetting: Refine definition - A physiology facility devoted to cardiovascular (http://en.wikipedia.org/wiki/Cardiovascular_disease) research. - - - version information - - The version information for the resource defined by a desc:Version_Information instance (containing information about version number, development stage and release date) - - - - Data output API for resource - - Data output - - data output - - - InteractionType - What type of interaction is this? - InteractionType - - - replacedBy - - - - - - AlgorithmPurpose - AlgorithmPurpose - Scientific purpose of algorithm - - - - Data input API for resource - - data input - Data input - - - related activities - - - - - - - - - - Related activity represented by a subclass of the activity:Activity class in the BRO -- multiple values allowed - - - - - related areas of research - Related area of research represented by a subclass of the area:Area_of_Research class in the BRO -- multiple values allowed - - - - Cross reference to another Resource Description, which describes a resource that is related in some way to this resource. - - - - MeasurementType - - what kind of information is being capture in this measurement? - MeasurementType - - - OutputForm - - What form of output is produced by this thing - OutputForm - - - - Resource type - resource type - - The class in the BRO that describes the type of the resource -- multiple values allowed - - - DocumentGoal - - What are the goals of the document - DocumentGoal - - - - - - - - Phone number contact for the resource - contact person phone - - - - Other Information - - Other_Information - - - - URL - The URL to access the resource - - - - The name of the resource - resource name - - Name - - - - Development stage (e.g. pre-alpha, alpha, beta, pre-release, release) - - Development stage - - development stage - - - - byline - - - - license - - - The license under which the resource is distributed - License model - - - Contact Person(s) - - The contact person for the resource - - contact person - - - publication identifier - Publication identifier for the resource from a publicly available publication database (e.g. PMID: 19483092 or doi: 10.1093/nar/gkp440). - - - - Definition - - - definition - - - Implementation_Language - Implementation Language - - - is this a peer-reviewed scientific publication? - PeerReviewStatus - PeerReviewStatus - - - - - - Research Program - Name of the research cluster as identified through a funding program or other generally-accepted organizational cluster (for example NCBC, CTSA, etc.) - research program - - - - contact person email - Email address contact for the resource - - - broad classification of protein type based on structure or function - ProteinType - ProteinType - - - Implementation Language - - language - - Software programming language in which resource was written or can be accessed - - - keywords - - The list of keywords - - choice of either many individual keyword elements or one element with comma-separated-values - - - - - resource sharable - Is this resource sharable [yes | no] - - - - - - platforms - The software platforms on which the resource was tested (for software resources) - Platforms tested - - - Type of biological transcript - TranscriptType - TranscriptType - - - - The version number - version - Version number - - - - Name and/or acronym of the research center or institute (if appropriate) that produced, shares, or uses the resource (usually a sub-unit of Organization) - Center or Institute - center - - - - - - documentation available - - - Is there available documentation [yes | no] - - - - - biositemap author - The person who edits or is responsible for the content of this biositemap file or of a particular resource description entry. - - - technical support - - What technical support is available [available | limited | none] - - - - - Organization - organization - Name of the organization that produced, shares, or uses the resource (for example Stanford University, University of Pittsburgh, etc.) - - - - Originator - - Originator of a class - Originator - - - - Date of release of version (can be specified as xsd:date or as an xsd:string) - release date - - - Target_User_Type - Target User Type - - - Identifier - Identifier - Any kind of identifier - - - - - Description - The description of the resource - description - - - - Deprecated for BRO v3.0 - - - Resource that provides access to software, applications, or toolkits that performs signal processing by repeated measures of the signal and then calculates the expected value of the data set. - Averaging and Aglomeration - - - - A resource the provides access to data about subjects in a clinical trial; for example demographics, medical history, labs, procedures, etc. - Clinical Trial Data - Deprecated for BRO v3.0 - - - - - - Environmental Health and Safety Resource - - - Centrality Analsysis - - - Deprecated for BRO v3.0 - - A Resource that provides access to a graph algorithm that uses ranking of network elements to identify the importance of elements in a network. - - - - - mailing list URL - - - - documentation URL - - - - TODO: - - - - diff --git a/test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl b/test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl deleted file mode 100644 index 27a0dcb..0000000 --- a/test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl +++ /dev/null @@ -1,31835 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]> - - - - - Dr. Arathi Raghunath - Molecular Connections Pvt. Ltd. - The Breast Cancer Cell Line Ontology is licensed under the terms of the Creative Commons Attribution License version 3.0 Unported, details at http://creativecommons.org/licenses/by/3.0/ - 3.0 - 05.August.2010 - http://creativecommons.org/licenses/by/3.0/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fluids and secretions - - Liquid substances produced by living organisms to fulfill specific functions or excreted as waste. - - - - - - - - body fluid - - Liquid components of living organisms. - - - - - - - - ascitic fluid - - - - - - - - - - - - - Ascitic_Fluids - - - - Effusion,_Peritoneal - - - - Effusions,_Peritoneal - - - - Fluid,_Ascitic - - - - Fluid,_Peritoneal - - - - Fluids,_Ascitic - - - - Fluids,_Peritoneal - - - - Peritoneal_Effusion - - - - Peritoneal_Effusions - - - - Peritoneal_Fluid - - - - Peritoneal_Fluids - - - - - - - - - - - The serous fluid of ascites, the accumulation of fluids in the peritoneal cavity. - - - - - - - - pericardial effusion - - - - - - - - - - - - - Chylopericardium - - - - Chylopericardiums - - - - Effusion,_Pericardial - - - - Effusions,_Pericardial - - - - Hemopericardium - - - - Pericardial_Effusions - - - - - Fluid accumulation within the pericardium. Serous effusions are associated with pericardial diseases. Hemopericardium is associated with trauma. Lipid-containing effusion (chylopericardium) results from leakage of thorasic duct. Severe cases can lead to cardiac tamponade. - - - - - - - - pleural effusion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Effusion,_Pleural - - - - Effusions,_Pleural - - - - Pleural_Effusions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Presence of fluid in the pleural cavity resulting from excessive transudation or exudation from the pleural surfaces. It is a sign of disease and not a diagnosis in itself. - - - - - - - - bio molecule - A biomolecule is any organic molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products. - - - - - - - - bacterial toxin - - A bacterial toxin is a type of toxin that is generated by bacteria. - - - - - - - - cholera endotoxin - - - - - - - - - hormone - - Chemical substances having a specific regulatory effect on the activity of a certain organ or organs. The term was originally applied to substances secreted by various endocrine glands and transported in the bloodstream to the target organs. It is sometimes extended to include those substances that are not produced by the endocrine glands but that have similar effects. - - - - - - - - adrenal cortex hormone - - Hormones secreted from Adrenal cortex. - - - - - - - - glucocorticoids - - - - - - - - - pancreatic hormone - - Hormones secreted from Pancreas - - - - - - - - proinsulin - - A pancreatic polypeptide of about 110 amino acids, depending on the species, that is the precursor of insulin. Proinsulin, produced by the pancreatic beta cells, is comprised sequentially of the N-terminal B-chain, the proteolytically removable connecting C-peptide, and the C-terminal A-chain. It also contains three disulfide bonds, two between A-chain and B-chain. After cleavage at two locations, insulin and C-peptide are the secreted products. Intact proinsulin with low bioactivity also is secreted in small amounts. - - - - - - - - insulin - - - - - - - - A 51-amino acid pancreatic hormone that plays a major role in the regulation of glucose metabolism, directly by suppressing endogenous glucose production (glycogenolysis; gluconeogenesis) and indirectly by suppressing glucagon secretion and lipolysis. Native insulin is a globular protein comprised of a zinc-coordinated hexamer. Each insulin monomer containing two chains, A (21 residues) and B (30 residues), linked by two disulfide bonds. Insulin is used as a drug to control insulin-dependent diabetes mellitus (Diabetes mellitus, type 1) - - - - - - - - protein - - Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. - - - - - - - - ar - - - - - - - - - - - - - - - - - - - AIS - - - - Androgen_receptor - - - - DHTR - - - - HUMARA - - - - HYSP1 - - - - KD - - - - NR3C4 - - - - SBMA - - - - SMAX1 - - - - TFM - - - - dihydrotestosterone_receptor - - - - - The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract causes spinal bulbar muscular atrophy (Kennedy disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Two alternatively spliced variants encoding distinct isoforms have been described. - - - - - - - - brca1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BRCA1/BRCA2-containing_complex,_subunit_1 - - - - BRCAI - - - - BRCC1 - - - - BROVCA1 - - - - IRIS - - - - PSCP - - - - RING_finger_protein_53 - - - - RNF53 - - - - breast_and_ovarian_cancer_susceptibility_protein_1 - - - - breast_and_ovarian_cancer_sususceptibility_protein - - - - breast_cancer_1,_early_onset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. - - - - - - - - calcr - - - - - - - CRT - - - - CTR - - - - CTR1 - - - - calcitonin receptor - - - - - - - - - - - This gene encodes a high affinity receptor for the peptide hormone calcitonin and belongs to a subfamily of seven transmembrane-spanning G protein-coupled receptors. The encoded protein is involved in maintaining calcium homeostasis and in regulating osteoclast-mediated bone resorption. Polymorphisms in this gene have been associated with variations in bone mineral density and onset of osteoporosis. Alternate splicing results in multiple transcript variants. - - - - - - - - ccnd1 - - - - - - - B-cell CLL/lymphoma 1 - - - - BCL1 - - - - CCND1 - - - - D11S287E - - - - G1/S-specific cyclin D1 - - - - PRAD1 - - - - U21B31 - - - - cyclin D1 - - - - - - - - - - - The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance throughout the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin forms a complex with and functions as a regulatory subunit of CDK4 or CDK6, whose activity is required for cell cycle G1/S transition. This protein has been shown to interact with tumor suppressor protein Rb and the expression of this gene is regulated positively by Rb. Mutations, amplification and overexpression of this gene, which alters cell cycle progression, are observed frequently in a variety of tumors and may contribute to tumorigenesis. - - - - - - - - cd44 - - - - - - - - - - - - - - - - - - - CD44 antigen - - - - CDW44 antigen - - - - GP90 lymphocyte homing/adhesion receptor - - - - Hermes antigen - - - - antigen gp90 homing receptor - - - - cell adhesion molecule - - - - cell surface glycoprotein CD44 - - - - chondroitin sulfate proteoglycan 8 - - - - extracellular matrix receptor-III - - - - hematopoietic cell E- and L-selectin ligand - - - - heparan sulfate proteoglycan - - - - homing function and Indian blood group system - - - - hyaluronate receptor - - - - phagocytic glycoprotein I - - - - - - - - - - - The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. - - - - - - - - cdc4 - - - - - - - - - - - - - - - cdh1 - - - - - - - Arc-1 - - - - CD324 - - - - CDH1 - - - - CDHE - - - - ECAD - - - - LCAM - - - - UVO - - - - cadherin 1, type 1, E-cadherin (epithelial) - - - - - - - - - - - - - - - - - - des - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CMD1I - - - - CSM1 - - - - CSM2 - - - - FLJ12025 - - - - FLJ39719 - - - - FLJ41013 - - - - FLJ41793 - - - - desmin - - - - intermediate filament protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a muscle-specific class III intermediate filament. Homopolymers of this protein form a stable intracytoplasmic filamentous network connecting myofibrils to each other and to the plasma membrane. Mutations in this gene are associated with desmin-related myopathy, a familial cardiac and skeletal myopathy (CSM), and with distal myopathies. - - - - - - - - egf - - - - - - - HOMG4 - - - - URG - - - - beta-urogastrone - - - - epidermal growth factor - - - - - Epidermal growth factor has a profound effect on the differentiation of specific cells in vivo and is a potent mitogenic factor for a variety of cultured cells of both ectodermal and mesodermal origin. The EGF precursor is believed to exist as a membrane-bound molecule which is proteolytically cleaved to generate the 53-amino acid peptide hormone that stimulates cells to divide. - - - - - - - - egfr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ERBB - - - - ERBB1 - - - - HER1 - - - - PIG61 - - - - avian erythroblastic leukemia viral oncogene homolog - - - - cell growth inhibiting protein 40 - - - - cell proliferation-inducing protein 61 - - - - epidermal growth factor receptor - - - - mENA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor. Binding of the protein to a ligand induces receptor dimerization and tyrosine autophosphorylation and leads to cell proliferation. Mutations in this gene are associated with lung cancer. - - - - - - - - epcam - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CO-17A - - - - CO17-1A - - - - EGP - - - - EGP-2 - - - - EGP34 - - - - EGP40 - - - - ESA - - - - Ep-CAM - - - - GA733-2 - - - - KS1/4 - - - - KSA - - - - M4S1 - - - - MIC18 - - - - MK-1 - - - - TACST-1 - - - - TACSTD1 - - - - TROP1 - - - - adenocarcinoma-associated antigen - - - - carcinoma-associated antigen GA733-2 - - - - epithelial cell adhesion molecule - - - - epithelial glycoprotein-2 - - - - hEGP-2 - - - - membrane component, chromosome 4, surface marker - - - - tumor-associated calcium signal transducer 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a carcinoma-associated antigen and is a member of a family that includes at least two type I membrane proteins. This antigen is expressed on most normal epithelial cells and gastrointestinal carcinomas and functions as a homotypic calcium-independent cell adhesion molecule. The antigen is being used as a target for immunotherapy treatment of human carcinomas. Mutations in this gene result in congenital tufting enteropathy. - - - - - - - - erbb2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CD340 - - - - HER-2 - - - - HER-2/neu - - - - HER2 - - - - NEU - - - - NGL - - - - TKR1 - - - - c-erb B2/neu protein - - - - erbB-2 - - - - herstatin - - - - neuroblastoma/glioblastoma derived oncogene homolog - - - - v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of downstream signalling pathways, such as those involving mitogen-activated protein kinase and phosphatidylinositol-3 kinase. Allelic variations at amino acid positions 654 and 655 of isoform a (positions 624 and 625 of isoform b) have been reported, with the most common allele, Ile654/Ile655, shown here. Amplification and/or overexpression of this gene has been reported in numerous cancers, including breast and ovarian tumors. Alternative splicing results in several additional transcript variants, some encoding different isoforms and others that have not been fully characterized. - - - - - - - - erbb3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ErbB-3 - - - - HER3 - - - - LCCS2 - - - - MDA-BF-1 - - - - MGC88033 - - - - c-erbB-3 - - - - c-erbB3 - - - - erbB-3 - - - - erbB3-S - - - - p180-ErbB3 - - - - p45-sErbB3 - - - - p85-sErbB3 - - - - v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 - - - - - This gene encodes a member of the epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases. This membrane-bound protein has a neuregulin binding domain but not an active kinase domain. It therefore can bind this ligand but not convey the signal into the cell through protein phosphorylation. However, it does form heterodimers with other EGF receptor family members which do have kinase activity. Heterodimerization leads to the activation of pathways which lead to cell proliferation or differentiation. Amplification of this gene and/or overexpression of its protein have been reported in numerous cancers, including prostate, bladder, and breast tumors. Alternate transcriptional splice variants encoding different isoforms have been characterized. One isoform lacks the intermembrane region and is secreted outside the cell. This form acts to modulate the activity of the membrane-bound form. Additional splice variants have also been reported, but they have not been thoroughly characterized. - - - - - - - - erbb4 - - - - - - - - - - - HER4 - - - - MGC138404 - - - - avian erythroblastic leukemia viral (v-erb-b2) oncogene homolog 4 - - - - p180erbB4 - - - - receptor tyrosine-protein kinase erbB-4 - - - - tyrosine kinase-type cell surface receptor HER4 - - - - v-erb-a erythroblastic leukemia viral oncogene homolog 4 - - - - - - - - - - - - - - - - - - - - - - - This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. It encodes a single-pass type I membrane protein with multiple cysteine rich domains, a transmembrane domain, a tyrosine kinase domain, a phosphotidylinositol-3 kinase binding site and a PDZ domain binding motif. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Multiple proteolytic events allow for the release of a cytoplasmic fragment and an extracellular fragment. Mutations in this gene have been associated with cancer. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. - - - - - - - - esr1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - DKFZp686N23123 - - - - ESRA - - - - Era - - - - NR3A1 - - - - estrogen receptor 1 - - - - estrogen receptor alpha - - - - - - - - - - - - - - - - - This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5' UTRs and use different promoters. - - - - - - - - estrogen receptor - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ER - - - - ESR - - - - Estradiol receptor - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Estrogen receptor is a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. - - - - - - - - fbxw7 - - - - - - - AGO - - - - CDC4 - - - - DKFZp686F23254 - - - - F-box and WD repeat domain containing 7 - - - - F-box and WD-40 domain protein 7 - - - - F-box protein FBW7 - - - - F-box protein SEL-10 - - - - FBW6 - - - - FBW7 - - - - FBX30 - - - - FBXO30 - - - - FBXW6 - - - - FLJ16457 - - - - SEL-10 - - - - SEL10 - - - - archipelago homolog - - - - archipelago, Drosophila, homolog of - - - - homolog of C elegans sel-10 - - - - - This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene was previously referred to as FBX30, and belongs to the Fbws class; in addition to an F-box, this protein contains 7 tandem WD40 repeats. This protein binds directly to cyclin E and probably targets cyclin E for ubiquitin-mediated degradation. Mutations in this gene are detected in ovarian and breast cancer cell lines, implicating the gene's potential role in the pathogenesis of human cancers. Three transcript variants encoding three different isoforms have been found for this gene. - - - - - - - - fgfr1 - - - - - - - - - - - - - - - - - BFGFR - - - - CD331 - - - - CEK - - - - FGFBR - - - - FLG - - - - FLJ99988 - - - - FLT2 - - - - FMS-like tyrosine kinase 2 - - - - HBGFR - - - - KAL2 - - - - N-SAM - - - - OGD - - - - OTTHUMP00000190881 - - - - basic fibroblast growth factor receptor 1 - - - - fibroblast growth factor receptor 1 - - - - fms-related tyrosine kinase 2 - - - - heparin-binding growth factor receptor - - - - hydroxyaryl-protein kinase - - - - soluble FGFR1 variant 1 - - - - soluble FGFR1 variant 2 - - - - - - - - - - - - - - - - - The protein encoded by this gene is a member of the fibroblast growth factor receptor (FGFR) family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member binds both acidic and basic fibroblast growth factors and is involved in limb induction. Mutations in this gene have been associated with Pfeiffer syndrome, Jackson-Weiss syndrome, Antley-Bixler syndrome, osteoglophonic dysplasia, and autosomal dominant Kallmann syndrome 2. Chromosomal aberrations involving this gene are associated with stem cell myeloproliferative disorder and stem cell leukemia lymphoma syndrome. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. - - - - - - - - fgfr2 - - - - - - - - - - - - - BEK - - - - BEK fibroblast growth factor receptor - - - - BFR-1 - - - - CD332 - - - - CEK3 - - - - CFD1 - - - - ECT1 - - - - FLJ98662; - - - - JWS - - - - K-SAM - - - - KGFR - - - - OTTHUMP00000020624 - - - - OTTHUMP00000020626 - - - - TK14 - - - - TK25 - - - - bacteria-expressed kinase - - - - fibroblast growth factor receptor 2 - - - - hydroxyaryl-protein kinase - - - - keratinocyte growth factor receptor - - - - protein tyrosine kinase, receptor like 14 - - - - soluble FGFR4 variant 4 - - - - - The protein encoded by this gene is a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member is a high-affinity receptor for acidic, basic and/or keratinocyte growth factor, depending on the isoform. Mutations in this gene are associated with Crouzon syndrome, Pfeiffer syndrome, Craniosynostosis, Apert syndrome, Jackson-Weiss syndrome, Beare-Stevenson cutis gyrata syndrome, Saethre-Chotzen syndrome, and syndromic craniosynostosis. Multiple alternatively spliced transcript variants encoding different isoforms have been noted for this gene. - - - - - - - - fgf receptors - - - - - - - FGF receptor - - - - FGFR - - - - - - - - - - - - - - - - - The fibroblast growth factor receptors consist of an extracellular ligand domain composed of three immunoglobulin-like domains, a single transmembrane helix domain, and an intracellular domain with tyrosine kinase activity. These receptors bind fibroblast growth factors, members of the largest family of growth factor ligands, comprising 22 members. So far, five distinct membrane FGFR have been identified in vertebrates and all of them belong to the tyrosine kinase superfamily (FGFR1 to FGFR4). - - - - - - - - fhit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AP3A hydrolase - - - - AP3Aase - - - - FRA3B - - - - bis(5'-adenosyl)-triphosphatase - - - - diadenosine 5',5'''-P1,P3-triphosphate hydrolase - - - - dinucleosidetriphosphatase - - - - fragile histidine triad gene - - - - tumor suppressor protein - - - - - This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas. Alternatively spliced transcript variants have been found for this gene. - - - - - - - - gfap - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FLJ45472 - - - - glial fibrillary acidic protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes one of the major intermediate filament proteins of mature astrocytes. It is used as a marker to distinguish astrocytes from other glial cells during development. Mutations in this gene cause Alexander disease, a rare disorder of astrocytes in the central nervous system. Alternative splicing results in multiple transcript variants encoding distinct isoforms. - - - - - - - - ins - - - - - - - ILPR - - - - IRDN - - - - insulin - - - - - After removal of the precursor signal peptide, proinsulin is post-translationally cleaved into two chains (peptide A and peptide B) that are covalently linked via two disulfide bonds. Binding of this mature form of insulin to the insulin receptor (INSR) stimulates glucose uptake. A variety of mutant alleles with changes in the coding region have been identified. There is a read-through gene, INS-IGF2, which overlaps with this gene at the 5' region and with the IGF2 gene at the 3' region. - - - - - - - - insr - - - - - - - - - - - - - CD220 - - - - HHF5 - - - - insulin receptor - - - - - - - - - - - After removal of the precursor signal peptide, the insulin receptor precursor is post-translationally cleaved into two chains (alpha and beta) that are covalently linked. Binding of insulin to the insulin receptor (INSR) stimulates glucose uptake. Two transcript variants encoding different isoforms have been found for this gene. - - - - - - - - krt10 - - - - - - - CK10 - - - - K10 - - - - KPP - - - - cytokeratin 10 - - - - keratin 10 - - - - - - - - - - - - - - - - - This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. - - - - - - - - krt13 - - - - - - - - - - - - - - - - - - - CK13 - - - - K13 - - - - MGC161462 - - - - MGC3781 - - - - cytokeratin 13 - - - - keratin 13 - - - - keratin, type I cytoskeletal 13 - - - - - The protein encoded by this gene is a member of the keratin gene family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. Most of the type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains. This type I cytokeratin is paired with keratin 4 and expressed in the suprabasal layers of non-cornified stratified epithelia. Mutations in this gene and keratin 4 have been associated with the autosomal dominant disorder White Sponge Nevus. The type I cytokeratins are clustered in a region of chromosome 17q21.2. Alternative splicing of this gene results in multiple transcript variants; however, not all variants have been described. - - - - - - - - krt14 - - - - - - - - - - - - - - - - - - - - - - - - - CK14 - - - - EBS3 - - - - EBS4 - - - - K14 - - - - NFJ - - - - cytokeratin 14 - - - - keratin 14 - - - - - - - - - - - This gene encodes a member of the keratin family, the most diverse group of intermediate filaments. This gene product, a type I keratin, is usually found as a heterotetramer with two keratin 5 molecules, a type II keratin. Together they form the cytoskeleton of epithelial cells. Mutations in the genes for these keratins are associated with epidermolysis bullosa simplex. At least one pseudogene has been identified at 17p12-p11. - - - - - - - - krt16 - - - - - - - - - - - - - CK16 - - - - FNEPPK - - - - K16 - - - - K1CP - - - - KRT16A; - - - - NEPPK - - - - cytokeratin 16 - - - - focal non-epidermolytic palmoplantar keratoderma - - - - keratin 16 - - - - keratin, type I cytoskeletal 16 - - - - - - - - - - - The protein encoded by this gene is a member of the keratin gene family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. Most of the type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains and are clustered in a region of chromosome 17q12-q21. This keratin has been coexpressed with keratin 14 in a number of epithelial tissues, including esophagus, tongue, and hair follicles. Mutations in this gene are associated with type 1 pachyonychia congenita, non-epidermolytic palmoplantar keratoderma and unilateral palmoplantar verrucous nevus. - - - - - - - - krt17 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - K17 - - - - PC - - - - PC2 - - - - PCHC1 - - - - cytokeratin-17 - - - - keratin 17 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes the type I intermediate filament chain keratin 17, expressed in nail bed, hair follicle, sebaceous glands, and other epidermal appendages. Mutations in this gene lead to Jackson-Lawler type pachyonychia congenita and steatocystoma multiplex. - - - - - - - - krt18 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CYK18 - - - - K18 - - - - cell proliferation-inducing protein 46 - - - - cytokeratin 18 - - - - keratin 18 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - KRT18 encodes the type I intermediate filament chain keratin 18. Keratin 18, together with its filament partner keratin 8, are perhaps the most commonly found members of the intermediate filament gene family. They are expressed in single layer epithelial tissues of the body. Mutations in this gene have been linked to cryptogenic cirrhosis. Two transcript variants encoding the same protein have been found for this gene. - - - - - - - - krt19 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 40-kDakeratinintermediatefilament - - - - CK19 - - - - K19 - - - - K1CS - - - - MGC15366 - - - - cytokeratin19 - - - - keratin,typeI,40-kd - - - - keratin,typeIcytoskeletal19 - - - - keratin19 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The protein encoded by this gene is a member of the keratin family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. The type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains. Unlike its related family members, this smallest known acidic cytokeratin is not paired with a basic cytokeratin in epithelial cells. It is specifically expressed in the periderm, the transiently superficial layer that envelopes the developing epidermis. The type I cytokeratins are clustered in a region of chromosome 17q12-q21. - - - - - - - - krt4 - - - - - - - CK4 - - - - CYK4 - - - - FLJ31692 - - - - K4 - - - - cytokeratin 4 - - - - keratin 4 - - - - keratin, type II cytoskeletal 4 - - - - - - - - - - - - - - - - - The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in differentiated layers of the mucosal and esophageal epithelia with family member KRT13. Mutations in these genes have been associated with White Sponge Nevus, characterized by oral, esophageal, and anal leukoplakia. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. - - - - - - - - krt7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CK7 - - - - K2C7 - - - - K7 - - - - MGC129731; - - - - MGC3625 - - - - SCL - - - - cytokeratin 7 - - - - keratin 7 - - - - keratin, 55K type II cytoskeletal - - - - keratin, simple epithelial type I, K7 - - - - keratin, type II cytoskeletal 7 - - - - sarcolectin - - - - type II mesothelial keratin K7 - - - - - - - - - - - - - - - - - - - - - - - The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the simple epithelia lining the cavities of the internal organs and in the gland ducts and blood vessels. The genes encoding the type II cytokeratins are clustered in a region of chromosome 12q12-q13. Alternative splicing may result in several transcript variants; however, not all variants have been fully described. - - - - - - - - krt8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CARD2 - - - - CK8 - - - - CYK8 - - - - K2C8 - - - - K8 - - - - KO - - - - cytokeratin 8 - - - - keratin 8 - - - - keratin, type II cytoskeletal 8 - - - - - This gene is a member of the type II keratin family clustered on the long arm of chromosome 12. Type I and type II keratins heteropolymerize to form intermediate-sized filaments in the cytoplasm of epithelial cells. The product of this gene typically dimerizes with keratin 18 to form an intermediate filament in simple single-layered epithelial cells. This protein plays a role in maintaining cellular structural integrity and also functions in signal transduction and cellular differentiation. Mutations in this gene cause cryptogenic cirrhosis. - - - - - - - - krt6 - - - - - - - - - - - - - - - - - - - CK6 - - - - KRT6 - - - - cytokeratin 6 - - - - - The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. As many as six of this type II cytokeratin (KRT6) have been identified; the multiplicity of the genes is attributed to successive gene duplication events. The genes are expressed with family members KRT16 and/or KRT17 in the filiform papillae of the tongue, the stratified epithelial lining of oral mucosa and esophagus, the outer root sheath of hair follicles, and the glandular epithelia. - - - - - - - - muc1 - - - - - - - - - - - - - - - - - - - - - - - CD227 - - - - DF3 antigen - - - - EMA - - - - H23 antigen - - - - H23AG - - - - KL-6 - - - - MAM6 - - - - MUC-1/SEC - - - - MUC-1/X - - - - MUC1/ZD - - - - PEM - - - - PEMT - - - - PUM - - - - breast carcinoma-associated antigen DF3 - - - - episialin - - - - mucin 1, cell surface associated - - - - mucin 1, transmembrane - - - - peanut-reactive urinary mucin - - - - polymorphic epithelial mucin - - - - tumor associated epithelial mucin - - - - - - - - - - - - - - - - - This gene is a member of the mucin family and encodes a membrane bound, glycosylated phosphoprotein. The protein is anchored to the apical surface of many epithelia by a transmembrane domain, with the degree of glycosylation varying with cell type. It also includes a 20 aa variable number tandem repeat (VNTR) domain, with the number of repeats varying from 20 to 120 in different individuals. The protein serves a protective function by binding to pathogens and also functions in a cell signaling capacity. Overexpression, aberrant intracellular localization, and changes in glycosylation of this protein have been associated with carcinomas. Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length nature of only some has been determined. - - - - - - - - muc2 - - - - - - - MLP - - - - SMUC - - - - mucin 2, intestinal/tracheal - - - - mucin 2, oligomeric mucus/gel-forming - - - - - - - - - - - This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. The protein polymerizes into a gel of which 80% is composed of oligosaccharide side chains by weight. The protein features a central domain containing tandem repeats rich in threonine and proline that varies between 50 and 115 copies in different individuals. Alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. - - - - - - - - myc - - - - - - - - - - - - - MRTL - - - - avian myelocytomatosis viral oncogene homolog - - - - bHLHe39 - - - - c-Myc - - - - myc proto-oncogene protein - - - - myc-related translation/localization regulatory factor - - - - v-myc avian myelocytomatosis viral oncogene homolog - - - - v-myc myelocytomatosis viral oncogene homolog - - - - - The protein encoded by this gene is a multifunctional, nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation. It functions as a transcription factor that regulates transcription of specific target genes. Mutations, overexpression, rearrangement and translocation of this gene have been associated with a variety of hematopoietic tumors, leukemias and lymphomas, including Burkitt lymphoma. There is evidence to show that alternative translation initiations from an upstream, in-frame non-AUG (CUG) and a downstream AUG start site result in the production of two isoforms with distinct N-termini. The synthesis of non-AUG initiated protein is suppressed in Burkitt's lymphomas, suggesting its importance in the normal function of this gene. - - - - - - - - mucin3 - - - - - - - - - - - - - MUC3 - - - - mucin 3 - - - - mucin 3, intestinal - - - - - The mucin genes encode epithelial glycoproteins, some of which are secreted and some membrane bound. Each of the genes contains at least one large domain of tandemly repeated sequence that encodes the peptide sequence rich in serine and/or threonine residues, which carries most of the O-linked glycosylation. - - - - - - - - nr3c1 - - - - - - - GR-A - - - - glucocorticoid receptor alpha - - - - nuclear receptor subfamily 3, group C, member 1 - - - - - - - - - - - - - - - - - - - - - - - Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription factor that binds to glucocorticoid response elements (GRE) and as a modulator of other transcription factors. Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Could act as a coactivator for STAT5-dependent transcription upon growth hormone (GH) stimulation and could reveal an essential role of hepatic GR in the control of body growth. Involved in chromatin remodeling. Plays a significant role in transactivation. Involved in nuclear translocation. - - - - - - - - nrg1 - - - - - - - - - - - - - - - - - ARIA - - - - GGF - - - - GGF2 - - - - HGL - - - - HRG - - - - HRG1 - - - - HRGA - - - - NDF - - - - SMDF - - - - glial growth factor - - - - heregulin, alpha (45kD, ERBB2 p185-activator) - - - - neu differentiation factor - - - - neuregulin 1 - - - - sensory and motor neuron derived factor - - - - - The protein encoded by this gene was originally identified as a 44-kD glycoprotein that interacts with the NEU/ERBB2 receptor tyrosine kinase to increase its phosphorylation on tyrosine residues. This protein is a signaling protein that mediates cell-cell interactions and plays critical roles in the growth and development of multiple organ systems. It is known that an extraordinary variety of different isoforms are produced from this gene through alternative promoter usage and splicing. These isoforms are tissue-specifically expressed and differ significantly in their structure, and thereby these isoforms are classified into types I, II, III, IV, V and VI. The gene dysregulation has been linked to diseases such as cancer, schizophrenia and bipolar disorder (BPD). - - - - - - - - pgr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NR3C3 - - - - PR - - - - progesterone receptor - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a member of the steroid receptor superfamily. The encoded protein mediates the physiological effects of progesterone, which plays a central role in reproductive events associated with the establishment and maintenance of pregnancy. This gene uses two distinct promotors and translation start sites in the first exon to produce two isoforms, A and B. The two isoforms are identical except for the additional 165 amino acids found in the N-terminus of isoform A only, and mediate their own response genes and physiologic effects with little overlap. The location of transcription initiation for isoform B has not been clearly determined. - - - - - - - - pten - - - - - - - 10q23del - - - - BZS - - - - MGC11227 - - - - MHAM - - - - MMAC1 - - - - MMAC1 phosphatase and tensin homolog deleted on chromosome 10 - - - - PTEN1 - - - - TEP1 - - - - mutated in multiple advanced cancers 1 - - - - phosphatase and tensin homolog - - - - - - - - - - - This gene was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. The protein encoded this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Unlike most of the protein tyrosine phosphatases, this protein preferentially dephosphorylates phosphoinositide substrates. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/PKB signaling pathway. - - - - - - - - p glycoprotein - - - - - - - - - - - - - ABCB - - - - MDR - - - - PGP - - - - - - - - - - - P-glycoprotein is a well-characterized ABC-transporter of the MDR/TAP subfamily. The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. - - - - - - - - tacc1 - - - - - - - - - - - - - DKFZp686K18126 - - - - FLJ42304 - - - - Ga55 - - - - KIAA1103 - - - - gastric cancer antigen Ga55 - - - - taxin 1 - - - - transforming, acidic coiled-coil containing protein 1 - - - - - This locus may represent a breast cancer candidate gene. It is located close to FGFR1 on a region of chromosome 8 that is amplified in some breast cancers. Three transcript variants encoding different isoforms have been found for this gene. - - - - - - - - tgfb1 - - - - - - - DPD1 - - - - ED - - - - LAP - - - - TGF-beta 1 protein - - - - TGFB - - - - TGFbeta - - - - diaphyseal dysplasia 1, progressive - - - - latency-associated peptide - - - - transforming growth factor, beta 1 - - - - - This gene encodes a member of the transforming growth factor beta (TGFB) family of cytokines, which are multifunctional peptides that regulate proliferation, differentiation, adhesion, migration, and other functions in many cell types. Many cells have TGFB receptors, and the protein positively and negatively regulates many other growth factors. The secreted protein is cleaved into a latency-associated peptide (LAP) and a mature TGFB1 peptide, and is found in either a latent form composed of a TGFB1 homodimer, a LAP homodimer, and a latent TGFB1-binding protein, or in an active form composed of a TGFB1 homodimer. The mature peptide may also form heterodimers with other TGFB family members. This gene is frequently upregulated in tumor cells, and mutations in this gene result in Camurati-Engelmann disease. - - - - - - - - tgfbr1 - - - - - - - AAT5 - - - - ACVRLK4 - - - - ALK-5 - - - - ALK5 - - - - LDS1A - - - - LDS2A - - - - SKR4 - - - - TGFR-1 - - - - activin A receptor type II-like kinase, 53kD - - - - activin A receptor type II-like kinase, 53kDa - - - - activin receptor-like kinase 5 - - - - serine/threonine-protein kinase receptor R4 - - - - transforming growth factor beta receptor I - - - - transforming growth factor, beta receptor 1 - - - - transforming growth factor, beta receptor I - - - - transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD) - - - - - - - - - - - - - - - - - The protein encoded by this gene forms a heteromeric complex with type II TGF-beta receptors when bound to TGF-beta, transducing the TGF-beta signal from the cell surface to the cytoplasm. The encoded protein is a serine/threonine protein kinase. Mutations in this gene have been associated with Loeys-Dietz aortic aneurysm syndrome (LDAS). Multiple transcript variants encoding different isoforms have been found for this gene. - - - - - - - - tgfbr2 - - - - - - - - - - - - - AAT3 - - - - FAA3 - - - - LDS1B - - - - LDS2B - - - - MFS2 - - - - RIIC - - - - TAAD2 - - - - TGF-beta receptor type IIB - - - - TGF-beta type II receptor - - - - TGFR-2 - - - - TGFbeta-RII - - - - transforming growth factor beta receptor type IIC - - - - transforming growth factor, beta receptor II - - - - - - - - - - - This gene encodes a member of the Ser/Thr protein kinase family and the TGFB receptor subfamily. The encoded protein is a transmembrane protein that has a protein kinase domain, forms a heterodimeric complex with another receptor protein, and binds TGF-beta. This receptor/ligand complex phosphorylates proteins, which then enter the nucleus and regulate the transcription of a subset of genes related to cell proliferation. Mutations in this gene have been associated with Marfan Syndrome, Loeys-Deitz Aortic Aneurysm Syndrome, and the development of various types of tumors. Alternatively spliced transcript variants encoding different isoforms have been characterized. - - - - - - - - tnf - - - - - - - - - - - - - - - - - - - - - - - - - APC1 protein - - - - DIF - - - - TNF superfamily, member 2 - - - - TNF, macrophage-derived - - - - TNF, monocyte-derived - - - - TNF-alpha - - - - TNFA - - - - TNFSF2 - - - - cachectin - - - - tumor necrosis factor - - - - tumor necrosis factor alpha - - - - - This gene encodes a multifunctional proinflammatory cytokine that belongs to the tumor necrosis factor (TNF) superfamily. This cytokine is mainly secreted by macrophages. It can bind to, and thus functions through its receptors TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. This cytokine is involved in the regulation of a wide spectrum of biological processes including cell proliferation, differentiation, apoptosis, lipid metabolism, and coagulation. This cytokine has been implicated in a variety of diseases, including autoimmune diseases, insulin resistance, and cancer. Knockout studies in mice also suggested the neuroprotective function of this cytokine. - - - - - - - - tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FLJ92943 - - - - LFS1 - - - - TRP53 - - - - p53 - - - - p53 antigen - - - - p53 transformation suppressor - - - - p53 tumor suppressor - - - - phosphoprotein p53 - - - - transformation-related protein 53 - - - - tumor protein p53 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes tumor protein p53, which responds to diverse cellular stresses to regulate target genes that induce cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. p53 protein is expressed at low level in normal cells and at a high level in a variety of transformed cell lines, where it's believed to contribute to transformation and malignancy. p53 is a DNA-binding protein containing transcription activation, DNA-binding, and oligomerization domains. It is postulated to bind to a p53-binding site and activate expression of downstream genes that inhibit growth and/or invasion, and thus function as a tumor suppressor. Mutants of p53 that frequently occur in a number of different human cancers fail to bind the consensus DNA binding site, and hence cause the loss of tumor suppressor activity. Alterations of this gene occur not only as somatic mutations in human malignancies, but also as germline mutations in some cancer-prone families with Li-Fraumeni syndrome. Multiple p53 variants due to alternative promoters and multiple alternative splicing have been found. These variants encode distinct isoforms, which can regulate p53 transcriptional activity. - - - - - - - - vim - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FLJ36605 - - - - vimentin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gene encodes a member of the intermediate filament family. Intermediate filamentents, along with microtubules and actin microfilaments, make up the cytoskeleton. The protein encoded by this gene is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. It is also involved in the immune response, and controls the transport of low-density lipoprotein (LDL)-derived cholesterol from a lysosome to the site of esterification. It functions as an organizer of a number of critical proteins involved in attachment, migration, and cell signaling. Mutations in this gene causes a dominant, pulverulent cataract. - - - - - - - - wnt3 - - - - - - - - - - - - - INT4 - - - - MGC131950 - - - - MGC138321 - - - - MGC138323 - - - - WNT-3 proto-oncogene protein - - - - wingless-type MMTV integration site family, member 3 - - - - - The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It encodes a protein which shows 98% amino acid identity to mouse Wnt3 protein, and 84% to human WNT3A protein, another WNT gene product. The mouse studies show the requirement of Wnt3 in primary axis formation in the mouse. Studies of the gene expression suggest that this gene may play a key role in some cases of human breast, rectal, lung, and gastric cancer through activation of the WNT-beta-catenin-TCF signaling pathway. This gene is clustered with WNT15, another family member, in the chromosome 17q21 region. - - - - - - - - wnt5a - - - - - - - WNT-5A protein - - - - hWNT5A - - - - wingless-type MMTV integration site family, member 5A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It encodes a protein which shows 98%, 98% and 87% amino acid identity to the mouse, rat and the xenopus Wnt5A protein, respectively. The experiments performed in Xenopus laevis embryos identified that human frizzled-5 (hFz5) is the receptor for the Wnt5A ligand and the Wnt5A/hFz5 signaling mediates axis induction. - - - - - - - - wnt7b - - - - - - - - - - - wingless-type MMTV integration site family, member 7B - - - This gene is a member of the WNT gene family, which consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. Among members of the human WNT family, this gene product is most similar to WNT7A protein. - - - - - - - - cell line - - - - - - - - normal cell line - - - - - - - - - - - - - - - - normal human cell line - - - - - - - - - 184 - - - - - - - - - - - - - - - 184A1 - - - - - - - 184-A1 - - - - 184_A1 - - - - - - - - CRL-8798 - - - - - - - - - - - - - - - - - - - - - - 184A1N4 - - - - - - - - - - - - - 184-A1N4 - - - - 184_A1N4 - - - - 184_A_1_N_4 - - - - - - - - - - - - 184B5 - - - - - - - - - - - - - 184-B5 - - - - 184_B5 - - - - - - - - CRL-8799 - - - - - - - - - - 184htrt - - - - - 184htert - - - - - - - - - - - - - - - - HBL100 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HBL-100 - - - - HBL_100 - - - - - - - - - - - - HMEC - - - - - - - - - - - - - - - Hs 190.T - - - - - CRL-7145 - - - - - - - - - - - - Hs190.T - - - - - - - - - - Hs 329.T - - - - - Hs329.T - - - - - - CRL-7242 - - - - - - - - - - - - - - - - Hs 344.T - - - - - CRL-7246 - - - - - - Hs344.T - - - - - - - - - - - - - - - - Hs 350.T - - - - - - - - - - - Hs350.T - - - - - - CRL-7248 - - - - - - - - - - Hs 371.T - - - - - - - - - - - CRL-7256 - - - - - - Hs371.T - - - - - - - - - - Hs 578Bst - - - - - - - - - - - - - - - - - HS578BST - - - - - - - - - - - - HTB-125 - - - - - - - - - - Hs 579.Mg - - - - - Hs579.Mg - - - - - - - - - - - - CRL-7347 - - - - - - - - - - Hs 617.Mg - - - - - CRL-7379 - - - - - - Hs617.Mg - - - - - - - - - - - - - - - - Hs 841.T - - - - - - - - - - - Hs841.T - - - - - - CRL-7574 - - - - - - - - - - hs 849.t - - - - - CRL-7583 - - - - - - Hs849.T - - - - - - - - - - - - - - - - hs 851.t - - - - - - - - - - - Hs851.T - - - - - - CRL-7584 - - - - - - - - - - hs 875.t - - - - - Hs875.T - - - - - - CRL-7612 - - - - - - - - - - - - - - - - m566 - - - - - - - - - - - - - - - mcf 10a myc - - - - - - - - - - - - - MCF10A-Myc - - - - c-Myc-MCF10A - - - - - MCF10A cells (human mammary epithelial cells) stably expressing c-Myc. - - - - - - - - mcf 10a - - - - - - - - - - - - - - - - - - - - - - - MCF-10A - - - - - - - - - - - - - - - - - - - - - - - - CRL-10317 - - - - - - - - - - - - - - - - - - - - - - - - - - - - svct - - - - - - - - - - - - - - - - - - - - - - - ECACC-94122105 - - - - - - - - - - - - - - - - - - - - - - fr2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 98031102 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fr5 - - - - - - - - - - - - - - - - - - - - - - - 98031103 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - htert-hme1 - - - - - CRL-4010 - - - - - - - - ME16C - - - - hTERTHME1 - - - - - - - - - - - - - - - - - Human non cancer breast epithelial cells immortalized by infection with the retrovirus pBabepuro+hTERT vectorline - - - - - - - - pathological cell line - - - - - - - - - - - - - - - pathological human cell line - - - - - - - - - hs 564(e).mg - - - - - Hs564(E).Mg - - - - - - - - - - - - - - - - - - CRL-7329 - - - - - - - - - - hs 566(b).t - - - - - - - - - - - - - - - - - CRL-7336 - - - - - - Hs566(B).T - - - - - - - - - - 600mpe - - - - - - - MPE-600 - - - - MPE600 - - - - MPE_600 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - au565 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2351 - - - - - - - - - - - - - - AU-565 - - - - AU_565 - - - - - - - - - - - - - - - - - - bcap37 - - - - - - - - - - - - - - - - - BCAP-37 - - - - - - - - - - brc-230 - - - - - - - - - - - - - BRC 230 - - - - BRC230 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - bt-20 - - - - - HTB-19 - - - - - - - - - - - - - - BT-20 - - - - BT_20 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - bt-474 - - - - - - - - - - - HTB-20 - - - - - - - - BT-474 - - - - BT_474 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 64 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ICLC_HTL00008 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - bt-483 - - - - - - - BT-483 - - - - BT_483 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-121 - - - - - - - - - - bt-549 - - - - - - - - - - - ICLC HTL02006 - - - - - - - - BT-549 - - - - BT_549 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-122 - - - - - - - - - - cal-120 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAL120 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cal-148 - - - - - ACC 460 - - - - - - - - - - - - - - - - - - CAL148 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cal-51 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAL51 - - - - - - - - - - - - - - - - - - - - - - cal-85-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAL851 - - - - - - - - - - cama-1 - - - - - HTB-21 - - - - - - - - - - - - - - - - - - - - - - - - - - CAMA-1 - - - - CAMA_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - colo-824 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - COLO824 - - - - - - - - - - - - - - - - du4475 - - - - - - - DU-4475 - - - - DU_4475 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-123 - - - - - - - - - - - - - - - - - - - - - - efm-19 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 231 - - - - - - - - - - - - - - - - - - - - - - - - EFM19 - - - - - - - - - - efm-192a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 258 - - - - - - - - - - - - EFM192A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - efm-192b - - - - - EFM192B - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 308 - - - - - - - - - - efm-192c - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 311 - - - - - - - - - - - - - - - - - - - - - - - - EFM192C - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - evsa-t - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gi-101a - - - - - - - - - - - GI101A - - - - - - - - - - - - - - - - - - - - - - - - - - - - h3922 - - - - - - - - - - - - - - - - - - - - - hcc1007 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1008 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1008 - - - - HCC_1008 - - - - - - - - - - - - - - CRL-2320 - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1143 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1143 - - - - HCC_1143 - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2321 - - - - - - - - - - - - - - - - - - - - - - hcc1187 - - - - - - - - - - - - - - - - - - - - - - - CRL-2322 - - - - - - - - - - - - - - - - - - - - HCC-1187 - - - - HCC_1187 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1395 - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1395 - - - - HCC_1395 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2324 - - - - - - - - - - hcc1419 - - - - - - - - - - - - - - - - - - - - - - - CRL-2326 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1419 - - - - HCC_1419 - - - - - - - - - - - - - - - - - - hcc1428 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1428 - - - - HCC_1428 - - - - - - - - - - - - - - - - - - - - CRL-2327 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1500 - - - - - - - - - - - - - HCC-1500 - - - - HCC_1500 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2329 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1569 - - - - - - - - - - - - - - - - - - - - - - - CRL-2330 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1569 - - - - HCC_1569 - - - - - - - - - - - - - - - - - - hcc1599 - - - - - CRL-2331 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1599 - - - - HCC_1599 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1739 - - - - - - - - - - - - - HCC-1739 - - - - HCC_1739 - - - - - - - - - - - - - - - - - - hcc1806 - - - - - - - - - - - - - - - - - CRL-2335 - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1806 - - - - HCC_1806 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1937 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2336 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-1937 - - - - HCC_1937 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc1954 - - - - - - - - - - - - - HCC-1954 - - - - HCC_1954 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2338 - - - - - - - - - - - - - - - - hcc202 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2316 - - - - - - - - HCC-202 - - - - HCC_202 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc2157 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2340 - - - - - - - - - - - - - - HCC-2157 - - - - HCC_2157 - - - - - - - - - - - - hcc2185 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-2185 - - - - HCC_2185 - - - - - - - - - - - - - - - - - - hcc2218 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC-2218 - - - - HCC_2218 - - - - - - - - - - - - - - CRL-2343 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc3153 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC_3153 - - - - - - - - - - hcc38 - - - - - - - - - - - - - - - - - HCC_38 - - - - - - CRL-2314 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hcc70 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2315 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HCC_70 - - - - - - - - - - - - - - - - - - - - - - hcc712 - - - - - HCC_712 - - - - - - - - - - - - - - - - - - - - - - hdq-p1 - - - - - - - - - - - - - - - - - - - - - - - HDQP1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 494 - - - - - - - - - - - - - - - - - - - - - - - - - - - - hmt-3909 - - - - - - - HMT 3909 - - - - HMT3909 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hs 274.t - - - - - CRL-7222 - - - - - - - - - - - - - - - - - - - - Hs-274.T - - - - Hs274.T - - - - - - - - - - - - hs 281.t - - - - - - - - - - - - - - - - - CRL-7227 - - - - - - - - Hs-281.T - - - - Hs281.T - - - - - - - - - - - - hs 319.t - - - - - - - Hs-319.T - - - - Hs319.T - - - - - - - - - - - - - - - - - - - - CRL-7236 - - - - - - - - - - hs 343.t - - - - - - - - - - - CRL-7245 - - - - - - - - - - - - - - Hs-343.T - - - - Hs343.T - - - - - - - - - - - - hs 362.t - - - - - CRL-7253 - - - - - - - - Hs-362.T - - - - Hs362.T - - - - - - - - - - - - - - - - - - - - - - - - hs 574.t - - - - - CRL-7345 - - - - - - - - - - - - - - Hs-574.T - - - - Hs574.T - - - - - - - - - - - - - - - - - - hs 578.t - - - - - - - - - - - - - - - - - HTB-126 - - - - - - - - - - - - Hs-578T - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hs 605.t - - - - - - - - - - - - - - - - - - - Hs-605.T - - - - Hs605.T - - - - - - - - CRL-7365 - - - - - - - - - - hs 606.t - - - - - - - Hs-606.T - - - - Hs606.T - - - - - - - - - - - - - - - - - - - - CRL-7368 - - - - - - - - - - hs 739.t - - - - - - - - - - - - - Hs-739.T - - - - Hs739.T - - - - - - - - - - - - - - CRL-7477 - - - - - - - - - - hs 741.t - - - - - CRL-7480 - - - - - - - - - - - - - - Hs-741.T - - - - Hs741.T - - - - - - - - - - - - - - - - - - hs 742.t - - - - - - - Hs-742.T - - - - Hs742.T - - - - - - - - - - - - - - - - - - - - CRL-7482 - - - - - - - - - - hs 748.t - - - - - - - - - - - - - - - - - CRL-7486 - - - - - - - - Hs-748.T - - - - Hs748.T - - - - - - - - - - - - hs 861.t - - - - - - - - - - - CRL-7596 - - - - - - - - Hs-861.T - - - - Hs861.T - - - - - - - - - - - - - - - - - - ibep-2 - - - - - - - - - - - - - - - - - IBEP2 - - - - - - - - - - - - - - - - ibh-6 - - - - - - - - - - - - - - - - - IBH6 - - - - - - - - - - ibh-7 - - - - - IBH7 - - - - - - - - - - - - - - - - - - - - - - jimt-1 - - - - - - - - - - - - - - - - - - - - - - - ACC 589 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - JIMT1 - - - - JIMT_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kpl-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - KPL1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ly2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - LY-2 - - - - - - - - - - m4a4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-2914 - - - - - - - - - - m4a4 gfp - - - - - - - - - - - CRL-2915 - - - - - - - - - - - - - - - - m4a4 lm3-2 gfp - - - - - - - - - - - - - - - - - CRL-2916 - - - - - - - - - - m4a4 lm3-4 cl16 gfp - - - - - - - - - - - - - - - - - CRL-2917 - - - - - - - - - - m7ts90 - - - - - - - - - - - - - - - - - - - - - mb 157 - - - - - - - - - - - - - MB-157 - - - - MB157 - - - - - - - - CRL-7721 - - - - - - - - - - - - - - - - - - - - - - mcf-10-2a - - - - - - - - - - - - - - - - - - - - - - - MCF10-2A - - - - - - - - - - - - - - - - - - CRL-10781 - - - - - - - - - - mcf-12a - - - - - - - - - - - - - - - - - - - - - - - MCF-12A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CRL-10782 - - - - - - - - - - - - - - - - mcf-12f - - - - - - - - - - - - - - - - - - - - - - - MCF12F - - - - - - CRL-10783 - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf-7 tam1 - - - - - MCF-7/TAMR-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf10ca1 - - - - - - - - - - - - - - - - - - - - - mcf10ca1a - - - - - - - - - - - - - - - - - - - - - mcf10ca1h - - - - - Ca1h - - - - - - - - - - - - - - - - - - - - - - mcf10dcis.com - - - - - - - - - - - - - - - - - - - - - mcf7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MCF-7 - - - - - - - - - - - - - - - - - - HTB-22 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MCF7-MVLN - - - - - - - - - - - - - - - - - - - - - - mcf7-382 - - - - - - - - - - - - - - - - - ICLC HTL95018 - - - - - - - - - - - - - - - - - - - - - - mcf7-422 - - - - - ICLC HTL95017 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf7-432 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ICLC HTL95019 - - - - - - - - - - mcf7-488x1 - - - - - - - - - - - - - - - - - ICLC HTL96004 - - - - - - MCF7488X1 - - - - - - - - - - - - - - - - - - - - - - mcf7-490x1 - - - - - - - - - - - ICLC HTL96002 - - - - - - - - - - - - MCF7490X1 - - - - - - - - - - - - - - - - - - - - - - mcf7-492x1 - - - - - - - - - - - - - - - - - - - - - - - MCF7492X1 - - - - - - ICLC HTL96028 - - - - - - - - - - - - - - - - mcf7/2a - - - - - - - - - - - MCF-7:2A - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf7/lcc1 - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf7/lcc2 - - - - - - - - - - - - - - - - - - - - - mcf7/lcc9 - - - - - - - - - - - - - - - - - LCC-9 - - - - - - - - - - - - - - - - - - - - - - mcf7:WS8 - - - - - - - - - - - - - - - - - - - - - mcf7 her2-18 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HER2-18 - - - - MCF-7/Her2-18 - - - - MCF7/HER2-18 - - - - - - - - - - - - - - - - - - - - - - - - mcf7a/z - - - - - - - - - - - - - - - - - MCF7A/Z - - - - - - - - - - - - - - - - mcf7adr - - - - - - - - - - - - - - - - - - - - - - - MCF-7/Adr - - - - - - - - - - - - - - - - mcf7e - - - - - - - - - - - - - - - - - - - MCF-7_early_passage - - - - MCF7E - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf7imIII - - - - - - - - - - - - - - - - - - - - - mcf7l - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MCF-7_late_passage - - - - MCF7L - - - - - - - - - - - - mcf7mp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mcf 10f - - - - - - - - - - - - - - - - - CRL-10318 - - - - - - - - - - - - - - - - - - - - - - - - MCF_10F - - - - - - - - - - - - - - - - mda-kb2 - - - - - - - - - - - - - - - - - CRL-2713 - - - - - - - - - - - - - - MDA_kb2 - - - - MDAkb2 - - - - - - - - - - - - - - - - - - mda-mb-134-VI - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-23 - - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB134VI - - - - MDA_MB_134_VI - - - - - - - - - - - - - - - - - - mda-mb-157 - - - - - HTB-24 - - - - - - - - MDAMB157 - - - - MDA_MB_157 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mda-mb-75-VII - - - - - - - - - - - - - - - - - - - MDAMB175VII - - - - MDA_MB_175_VII - - - - - - - - HTB-25 - - - - - - - - - - - - - - - - - - - - - - - - - - - - mda-mb-231 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-26 - - - - - - - - MDAMB231 - - - - MDA_MB_231 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mda-mb-231-5a-d - - - - - - - - - - - - - - - - - MDA-231-D - - - - - - - - - - - - - - - - mda-mb-231-5a - - - - - - - - - - - - - - - - - MDA-5a - - - - - - - - - - - - - - - - mda-mb-330 - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB330 - - - - MDA_MB_330 - - - - - - - - HTB-127 - - - - - - - - - - mda-mb-361 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB361 - - - - MDA_MB_361 - - - - - - - - - - - - - - - - - - - - HTB-27 - - - - - - - - - - - - - - - - mda-mb-415 - - - - - HTB-128 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB415 - - - - MDA_MB_415 - - - - - - - - - - - - mda-mb-436 - - - - - - - - - - - HTB-130 - - - - - - - - - - - - - - - - - - - - MDAMB436 - - - - MDA_MB_436 - - - - - - - - - - - - - - - - - - - - - - - - mda-mb-453 - - - - - - - - - - - HTB-131 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB453 - - - - MDA_MB_453 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mda-mb-468 - - - - - - - - - - - - - - - - - - - - - - - - - MDAMB468 - - - - MDA_MB_468 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-132 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mda468 clone nq16 - - - - - - - - - - - - - MDA468/NQ16 - - - - MDA468_NQ16 - - - - NQ16 - - - - - - - - - - - - - - - - - - - - - - - - mfm-223 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 422 - - - - - - - - - - - - MFM223 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mt-3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACC 403 - - - - - - - - - - - - - - - - - - - - - - - - MT3 - - - - - - - - - - - - - - - - - - - - - - mvln - - - - - - - - - - - - - - - - - - - - - mx-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nm2c5 - - - - - - - - - - - CRL-2918 - - - - - - - - - - - - - - - - - - - - - - - - - - - - nm2c5 gfp - - - - - - - - - - - CRL-2919 - - - - - - - - - - - - - - - - - - - - - - - - - - - - ocub-f - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sk-br-3 - - - - - - - - - - - - - SKBR3 - - - - SK_BR_3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HTB-30 - - - - - - - - - - - - ICLC HTL03005 - - - - - - - - - - - - - - - - - - - - - - - - - - - - sk-br-5 - - - - - - - - - - - - - SKBR5 - - - - SK_BR_5 - - - - - - - - - - - - - - - - - - sk-br-7 - - - - - - - - - - - - - - - - - - - SKBR7 - - - - SK_BR_7 - - - - - - - - - - - - sum102pt - - - - - - - - - - - SUM-102PT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum1315mo2 - - - - - SUM-1315MO2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum149pt - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SUM-149 - - - - SUM-149PT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum159pt - - - - - SUM-159PT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum185pe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SUM-185PE - - - - - - - - - - - - - - - - sum190pt - - - - - - - - - - - SUM-190PT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum225cwn - - - - - SUM-225CWN - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sum229pe - - - - - - - - - - - - - - - - - SUM-229PE - - - - - - - - - - - - - - - - sum44pe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SUM-44PE - - - - - - - - - - sum52pe - - - - - - - SUM-52PE - - - - SUM52 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sw527 - - - - - - - - - - - CRL-7940 - - - - - - - - - - - - - - SW-527 - - - - SW_527 - - - - - - - - - - - - t-47d - - - - - - - - - - - - - - - - - 85102201 - - - - - - - - - - - - - - - - - - HTB-133 - - - - - - - - - - - - - - - - - - - - - - - - T47D - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ICLC HTL98003 - - - - - - - - - - - - - - - - - - - - - - t47d-kbluc - - - - - - - - - - - - - - - - - - - - - - - CRL-2865 - - - - - - - - - - t47d/a1-2 - - - - - - - - - - - - - - - - - - - - - - - - - T-47D/A1-2 - - - - T47D(A1-2) - - - - - - - - - - - - tse - - - - - - - - - - - - - - - - - - - - - uacc-812 - - - - - - - - - - - - - - - - - - - - - - - CRL-1897 - - - - - - - - - - - - - - - - - - - - - - - - UACC812 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - uacc-893 - - - - - - - - - - - - - - - - - CRL-1902 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - UACC893 - - - - - - - - - - ymb-1 - - - - - - - - - - - - - - - - - - - - - ymb-a - - - - - - - - - - - - - - - - - - - - - ymb-s - - - - - - - - - - - - - - - - - - - - - zr-75-1 - - - - - 87012601 - - - - - - - - - - - - CRL-1500 - - - - - - - - - - - - - - - - - - ZR75-1 - - - - - - - - - - - - - - - - - - ICLC HTL99006 - - - - - - - - - - - - - - - - - - - - - - - - - - - - zr-75-1 dox - - - - - - - - - - - - - - - - - - - - - zr-75-27 - - - - - - - - - - - - - - - - - - - - - - - - - - - zr-75-30 - - - - - 88113004 - - - - - - - - - - - - - - - - - - CRL-1504 - - - - - - - - - - - - ZR7530 - - - - - - - - - - - - - - - - - - - - - - - - - - - - zr-75-9a1 - - - - - - - - - - - - - - - - - - - - - zr-pr-lt - - - - - - - - - - - - - - - - - - - - - zr75b - - - - - - - - - - - - - - - - - - - - - - - ZR-75-B - - - - - - - - - - - - - - - - pathological mouse cell line - - - - - - - - - 4t1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The 4T1 cell line was derived from a spontaneously arising BALB/c mammary tumor - - - - - - - - chemicals and drugs - - - - - - - - hormone antagonists - - Inhibitors of hormonal activity - - - - - - - - antiestrogens - - Inhibitors of estrogen hormone activity - - - - - - - - ici 164384 - - - - - - - - - - - - - ICI 164,384 - - - - ICI M164384 - - - - N-n-Butyl-N-methyl-11-(3,17beta-dihydroxyestra-1,3,5(10)-trien-7alpha-yl)undecanamide - - - - - - - - - - - - - ici 182780 - - - - - - - 7alpha-(9-((4,4,5,5,5-Pentafluoropentyl)sulfinyl)nonyl)estra-1,3,5(10)-triene-3,17beta-diol - - - - CCRIS 8741 - - - - Faslodex - - - - Fulvestrant - - - - HSDB 7658 - - - - ICI 182,780 - - - - ICI 182780 - - - - UNII-22X328QOC4 - - - - ZM 182780 - - - - - - - - - - - - - - - - - - lipid - - A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. - - - - - - - - fatty acid - - - - - - - Acids, Aliphatic - - - - Acids, Esterified Fatty - - - - Acids, Fatty - - - - Acids, Saturated Fatty - - - - Aliphatic Acids - - - - Esterified Fatty Acids - - - - Fatty Acids, Esterified - - - - Fatty Acids, Saturated - - - - Saturated Fatty Acids - - - - - Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated. - - - - - - - - mycophenolic acid - - - - - - - - - - - - - EINECS 207-595-8 - - - - UNII-HU9DX48N0T - - - - - - - - - - - - organic chemicals - - A broad class of substances containing carbon and its derivatives. Many of these chemicals will frequently contain hydrogen with or without oxygen, nitrogen, sulfur, phosphorus, and other elements. They exist in either carbon chain or carbon ring form. - - - - - - - - hydrocarbons - - - - - - - - - terpenes - - - - - - - Isoprenoids - - - - Terpenoids - - - - - A class of compounds composed of repeating 5-carbon units of hemiterpenes - - - - - - - - carotenoids - - - - - - - Carotene - - - - Carotenes - - - - - The general name for a group of fat-soluble pigments found in green, yellow, and leafy vegetables, and yellow fruits. They are aliphatic hydrocarbons consisting of a polyisoprene backbone. - - - - - - - - retinoids - - A group of tetraterpenes, with four terpene units joined head-to-tail. Biologically active members of this class are used clinically in the treatment of severe cystic acne; psoriasis; and other disorders of keratinization. - - - - - - - - vitamin a - - - - - - - 11-cis-Retinol - - - - 3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraen-1-ol, (all-E)-Isomer - - - - All Trans Retinol - - - - All-Trans-Retinol - - - - Aquasol A - - - - Retinol - - - - Vitamin A1 - - - - - Retinol and derivatives of retinol that play an essential role in metabolic functioning of the retina, the growth of and differentiation of epithelial tissue, the growth of bone, reproduction, and the immune response. Dietary vitamin A is derived from a variety of carotenoids found in plants. It is enriched in the liver, egg yolks, and the fat component of dairy products. - - - - - - - - tretinoin - - - - - - - Acid, Retinoic - - - - Acid, Vitamin A - - - - Acid, all-trans-Retinoic - - - - Acid, beta-all-trans-Retinoic - - - - Acid, trans-Retinoic - - - - Potassium Salt, Tretinoin - - - - Retin A - - - - Retin-A - - - - Retinoic Acid - - - - Salt, Tretinoin Potassium - - - - Salt, Tretinoin Sodium - - - - Salt, Tretinoin Zinc - - - - Sodium Salt, Tretinoin - - - - Tretinoin Potassium Salt - - - - Tretinoin Sodium Salt - - - - Tretinoin Zinc Salt - - - - Vesanoid - - - - Vitamin A Acid - - - - Zinc Salt, Tretinoin - - - - all trans Retinoic Acid - - - - all-trans-Retinoic Acid - - - - beta all trans Retinoic Acid - - - - beta-all-trans-Retinoic Acid - - - - trans Retinoic Acid - - - - trans-Retinoic Acid - - - - - - - - - - - An important regulator of gene expression during growth and development, and in neoplasms. Tretinoin, also known as retinoic acid and derived from maternal vitamin A, is essential for normal growth; and embryonic development. An excess of tretinoin can be teratogenic. It is used in the treatment of psoriasis; acne vulgaris; and several other skin diseases. It has also been approved for use in promyelocytic leukemia (leukemia, promyelocytic, acute). - - - - - - - - diterpenes - - - - - - - Cembrane Diterpenes - - - - Cembranes - - - - Diterpenes, Cembrane - - - - Diterpenes, Labdane - - - - Diterpenoids - - - - Labdane Diterpenes - - - - Labdanes - - - - Norditerpenes - - - - Norditerpenoids - - - - - Twenty-carbon compounds derived from mavalonic acid or deoxyxylulose phosphate. - - - - - - - - phorbols - - The parent alcohol of the tumor promoting compounds from croton oil (Croton tiglium). - - - - - - - - phorbol esters - - - - - - - Diesters, Phorbol - - - - Esters, Phorbol - - - - Phorbol Diesters - - - - - Tumor-promoting compounds obtained from croton oil (Croton tiglium). Some of these are used in cell biological experiments as activators of protein kinase C. - - - - - - - - tetradecanoylphorbol acetate - - - - - - - - - - - - - 12 Myristoyl 13 acetylphorbol - - - - 12 O Tetradecanoyl Phorbol 13 Acetate - - - - 12-Myristoyl-13-acetylphorbol - - - - 12-O-Tetradecanoyl Phorbol 13-Acetate - - - - 13-Acetate, 12-O-Tetradecanoyl Phorbol - - - - Acetate, Phorbol Myristate - - - - Acetate, Tetradecanoylphorbol - - - - Myristate Acetate, Phorbol - - - - Phorbol 13-Acetate, 12-O-Tetradecanoyl - - - - Phorbol Myristate Acetate - - - - Tetradecanoylphorbol Acetate, 4a alpha Isomer - - - - Tetradecanoylphorbol Acetate, 4a alpha-Isomer - - - - - A phorbol ester found in croton oil with very effective tumor promoting activity. It stimulates the synthesis of both DNA and RNA. - - - - - - - - receptor antagonists - - Compounds inhibiting receptor activity - - - - - - - - erbb2 inhibitors - - Compounds inhibitng ERBB2 receptor activity. - - - - - - - - therapeutic agent - - Compounds used in treatment of various pathological conditions. - - - - - - - - antibacterial agent - - - - - - - Agents, Anti-Bacterial - - - - Agents, Anti-Mycobacterial - - - - Agents, Antibacterial - - - - Agents, Antimycobacterial - - - - Agents, Bacteriocidal - - - - Anti Bacterial Agents - - - - Anti Mycobacterial Agents - - - - Anti-Mycobacterial Agents - - - - Antibacterial Agents - - - - Antibiotics - - - - Antimycobacterial Agents - - - - Bacteriocidal Agents - - - - Bacteriocides - - - - - Substances that reduce the growth or reproduction of bacteria. - - - - - - - - geneticin - - - - - - - Antibiotic G418 - - - - BRN 1669188 - - - - G 418 - - - - - - - - - - - - zeocin - - - - - - - (4-Oxo-5-(phenylmethoxy)-4H-pyran-2-yl)methyl thiocyanate - - - - 5-Benzyloxy-2-thiocyanatomethyl-4-pyranone - - - - 5-Bz-2-Scnm-4-pyranone - - - - Zeomycin - - - - - Zeocin is a member of the bleomycin/phleomycin family of antibiotics, known to bind and cleave DNA. - - - - - - - - antineoplastic agent - - - - - - - - - doxorubicin - - - - - - - Adriablastin - - - - Adriablastine - - - - Adriamycin - - - - Adriblastin - - - - Adriblastina - - - - Adriblastine - - - - Adrimedac - - - - Baxter Brand of Doxorubicin Hydrochloride - - - - Bristol-Myers Squibb Brand of Doxorubicin Hydrochloride - - - - Caelyx - - - - Columbia Brand of Doxorubicin Hydrochloride - - - - DOX SL - - - - DOX-SL - - - - DOXO cell - - - - DOXO-cell - - - - Doxil - - - - Doxolem - - - - Doxorubicin Hexal - - - - Doxorubicin Hydrochloride - - - - Doxorubicin NC - - - - Doxorubicin, Liposomal - - - - Doxorubicina Ferrer Farm - - - - Doxorubicina Funk - - - - Doxorubicina Tedec - - - - Doxorubicine Baxter - - - - Doxotec - - - - Elan Brand of Doxorubicin Hydrochloride - - - - Essex Brand of Doxorubicin Hydrochloride - - - - Farmiblastina - - - - Ferrer Brand of Doxorubicin Hydrochloride - - - - Hexal Brand of Doxorubicin Hydrochloride - - - - Hydrochloride, Doxorubicin - - - - Kenfarma Brand of Doxorubicin Hydrochloride - - - - Lemery Brand of Doxorubicin Hydrochloride - - - - Liposomal Doxorubicin - - - - Myocet - - - - Neocorp Brand of Doxorubicin Hydrochloride - - - - Onkodox - - - - Onkoworks Brand of Doxorubicin Hydrochloride - - - - Ortho Biotech Brand of Doxorubicin Hydrochloride - - - - Pharmacia Brand of Doxorubicin Hydrochloride - - - - Prasfarma Brand of Doxorubicin Hydrochloride - - - - Ribodoxo - - - - Rubex - - - - Schering Brand of Doxorubicin Hydrochloride - - - - Schering-Plough Brand of Doxorubicin Hydrochloride - - - - Tedec Meiji Brand of Doxorubicin Hydrochloride - - - - Urokit Doxo cell - - - - Urokit Doxo-cell - - - - cell pharm Brand of Doxorubicin Hydrochloride - - - - medac Brand of Doxorubicin Hydrochloride - - - - ribosepharm Brand of Doxorubicin Hydrochloride - - - - - Antineoplastic antibiotic obtained from Streptomyces peucetius. It is a hydroxy derivative of daunorubicin. - - - - - - - - epirubicin - - - - - - - 4' Epi Adriamycin - - - - 4' Epi DXR - - - - 4' Epi Doxorubicin - - - - 4' Epiadriamycin - - - - 4' Epidoxorubicin - - - - 4'-Epi-Adriamycin - - - - 4'-Epi-DXR - - - - 4'-Epi-Doxorubicin - - - - 4'-Epiadriamycin - - - - 4'-Epidoxorubicin - - - - EPI-cell - - - - Ellence - - - - Epilem - - - - Epirubicin Hydrochloride - - - - Farmorubicin - - - - Farmorubicina - - - - Farmorubicine - - - - Hydrochloride, Epirubicin - - - - IMI 28 - - - - IMI-28 - - - - IMI28 - - - - Kenfarma Brand of Epirubicin Hydrochloride - - - - Lemery Brand of Epirubicin Hydrochloride - - - - NSC 256942 - - - - NSC-256942 - - - - NSC256942 - - - - Pharmacia Brand of Epirubicin Hydrochloride - - - - Pharmorubicin - - - - cell pharm Brand of Epirubicin - - - - - An anthracycline which is the 4'-epi-isomer of doxorubicin. The compound exerts its antitumor effects by interference with the synthesis and function of DNA. - - - - - - - - etoposide - - - - - - - Baxter Brand of Etoposide - - - - Baxter Oncology Brand of Etoposide - - - - Bristol Myers Brand of Etoposide - - - - Bristol Myers Squibb Brand of Etoposide - - - - Bristol-Myers Brand of Etoposide - - - - Bristol-Myers Squibb Brand of Etoposide - - - - Celltop - - - - Demethyl Epipodophyllotoxin Ethylidine Glucoside - - - - Eposide - - - - Eposin - - - - Eto CS - - - - Eto GRY - - - - Eto-GRY - - - - Etomedac - - - - Etopos - - - - Etoposide Pierre Fabre - - - - Etoposide Teva - - - - Etoposide, (5S)-Isomer - - - - Etoposide, (5a alpha)-Isomer - - - - Etoposide, (5a alpha,9 alpha)-Isomer - - - - Etoposide, alpha D Glucopyranosyl Isomer - - - - Etoposide, alpha-D-Glucopyranosyl Isomer - - - - Etoposido Ferrer Farma - - - - Exitop - - - - Ferrer Brand of Etoposide - - - - Gry Brand of Etoposide - - - - Lastet - - - - Lemery Brand of Etoposide - - - - Medac Brand of Etoposide - - - - NSC 141540 - - - - NSC-141540 - - - - NSC141540 - - - - Novartis Brand of Etoposide - - - - Onkoposid - - - - Onkoworks Brand of Etoposide - - - - Pharmachemie Brand of Etoposide - - - - Pharmacia Brand of Etoposide - - - - Pierre Fabre Brand of Etoposide - - - - Prasfarma Brand of Etoposide - - - - Riboposid - - - - Sanfer Brand of Etoposide - - - - Tedec Meiji Brand of Etoposide - - - - Teva Brand of Etoposide - - - - Toposar - - - - VP 16 - - - - VP 16 213 - - - - VP 16-213 - - - - VP 16213 - - - - VP-16 - - - - VP16 - - - - Vepesid - - - - Vépéside Sandoz - - - - Vépéside-Sandoz - - - - alpha-D-Glucopyranosyl Isomer Etoposide - - - - ribosepharm Brand of Etoposide - - - - - A semisynthetic derivative of podophyllotoxin that exhibits antitumor activity. Etoposide inhibits DNA synthesis by forming a complex with topoisomerase II and DNA. This complex induces breaks in double stranded DNA and prevents repair by topoisomerase II binding. Accumulated breaks in DNA prevent entry into the mitotic phase of cell division, and lead to cell death. Etoposide acts primarily in the G2 and S phases of the cell cycle. - - - - - - - - idarubicinol - - - - - - - 13-dihydroidarubicin - - - - 4-demethoxy-14-hydroxydaunorubicin - - - - idarubicinol, (7S-(7alpha,9alpha,9(S*)))-isomer - - - - - - - - - - - - mitoxantrone - - - - - - - AHP Brand of Mitoxantrone Hydrochloride - - - - ASTA Medica Brand of Mitoxantrone Hydrochloride - - - - Acetate, Mitoxantrone - - - - Amgen Brand of Mitoxantrone Hydrochloride - - - - Baxter Oncology Brand of Mitoxantrone Hydrochloride - - - - CL 232325 - - - - CL-232325 - - - - CL232325 - - - - Columbia Brand of Mitoxantrone Hydrochloride - - - - DHAQ - - - - Hydrochloride, Mitoxantrone - - - - Inibsa Brand of Mitoxantrone Hydrochloride - - - - Lederle Brand of Mitoxantrone Hydrochloride - - - - Mitoxantrone Acetate - - - - Mitoxantrone Hydrochloride - - - - Mitozantrone - - - - Mitroxone - - - - NSC 279836 - - - - NSC 287836 - - - - NSC 299195 - - - - NSC 301739 - - - - NSC 301739D - - - - NSC-279836 - - - - NSC-287836 - - - - NSC-299195 - - - - NSC-301739 - - - - NSC-301739D - - - - NSC279836 - - - - NSC287836 - - - - NSC299195 - - - - NSC301739 - - - - NSC301739D - - - - Novantron - - - - Novantrone - - - - Onkotrone - - - - Pralifan - - - - Ralenova - - - - Wyeth Brand of Mitoxantrone Hydrochloride - - - - - An anthracenedione-derived antineoplastic agent. - - - - - - - - genetic variation - - - - - - - - chromosomal mutation - - - - - - - - - chromosomal deletion - - - - - - - - - deletion in long arm - - - - - - - - - - deletion in short arm - - - - - - - - - homozygous deletion at 3p12 - - - - - - - - - - - - - - - - - - - - - homozygous deletion at 3p14.2 - - - - - - - - - - - - - - - - - - - - - homozygous deletion at 3p21.3 - - - - - - - - - - - - - - - - - - - - - gene mutation - - - - - - - - - deletion - - - - - - - - - exon deletion - - - - - - - - - exon2 deletion in cdh1 - - - - - - - - - - - - - - - - - - - - - - - - - - - exon5 deletion in estrogen receptor - - - - - - - - - - - - - - - - - - - - - - - - - - - exon9 deletion in cdh1 - - - - - - - - - - - - - - - - - - - - - - - - - - - homozygous deletion of fhit gene - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - homozygous deletion of pten gene - - - - - - - - - - - - - - - - - - - - - - - - - - - duplication - - - - - - - - - exon duplication - - - - - - - - - exon8 duplication in cdc4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - exon9 duplication in cdc4 - - - - - - - - - - - - - - - - - - - - - - - - - - - gene duplication - - - - - - - - - ccnd1 gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - erbb2 gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fgfr1 gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fgfr2 gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - myc gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - tacc1 gene amplification - - - - - - - - - - - - - - - - - - - - - - - - - - - insertion - - - - - - - - - 5382ins c in brca1 - - - - - - - - - - - - - - - - - - - - - - - - - - - 943ins 10bp in brca1 - - - - - - - - - - - - - - - - - - - - - - - - - - - point mutation - - - - - - - - - nonsense mutation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - transition - - - - - - - - - codon 175 in exon5 cgc to cac in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon 194 in exon6 ctt to ttt in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon248 in exon7 cgg to cag in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon249 in exon7 agg to ggg in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon273 in exon8 cgt to cat in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - codon280 in exon8 aga to aaa in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon283 in exon8 cgc to tgc in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon285 in exon8 gag to aag in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - transversion - - - - - - - - - codon132 in exon5 aag to cag in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon157 in exon5 gtc to ttc in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon249 in exon7 agg to agc in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon273 in exon8 cgt to ctt in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon280 in exon8 aga to aca in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - codon281 in exon8 gac to cac in tp53 - - - - - - - - - - - - - - - - - - - - - - - - - - - nucleotide651 g to t in fhit - - - - - - - - - - - - - - - - - - - - - - - - - - - pathological condition - - - - - - - - neoplasms - - New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms. - - - - - - - - papillary invasive ductal tumor - - - - - - - - - - - - - - - - - - - - Invasive form of papillary ductal cercinoma of the breast. - - - - - - - - noninvasive breast carcinoma - - Benign tumors of the breast. - - - - - - - - ductal carcinoma in situ - - - - - - - - - - - - - Carcinoma, Intraductal - - - - Carcinoma, Intraductal, Noninfiltrating - - - - Carcinoma, Noninfiltrating Intraductal - - - - Carcinomas, Intraductal - - - - Carcinomas, Noninfiltrating Intraductal - - - - DCIS - - - - Intraductal Carcinoma - - - - Intraductal Carcinoma, Noninfiltrating - - - - Intraductal Carcinomas - - - - Intraductal Carcinomas, Noninfiltrating - - - - Noninfiltrating Intraductal Carcinoma - - - - Noninfiltrating Intraductal Carcinomas - - - - - - - - - - - A noninvasive (noninfiltrating) carcinoma of the breast characterized by a proliferation of malignant epithelial cells confined to the mammary ducts or lobules, without light-microscopy evidence of invasion through the basement membrane into the surrounding stroma. - - - - - - - - lobular carcinoma in situ - - Although the name includes the term carcinoma, lobular carcinoma in situ (LCIS) is not really cancer, but rather a noninvasive condition that increases the risk of developing cancer in the future. LCIS, also known as lobular neoplasia or stage 0 breast cancer, occurs when abnormal cells accumulate in the breast lobules. Each breast has hundreds of milk producing lobules, which are connected to the milk ducts. In LCIS, the abnormal cells are often found throughout the breast lobules and both breasts are affected about 30 percent of the time. - - - - - - - - acantholytic squamous cell carcinoma of breast - - - - - - - - Primary acantholytic squamous cell carcinoma (ASCC) of the breast is a rare and aggressive variant of invasive breast cancer. - - - - - - - - adenocarcinoma of breast - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Adenocarcinoma of the breast. - - - - - - - - breast disease - - - - - - - Breast Disease - - - - Breast Disease, Endocrine - - - - Breast Diseases, Endocrine - - - - Disease, Breast - - - - Disease, Endocrine Breast - - - - Diseases, Breast - - - - Diseases, Endocrine Breast - - - - Endocrine Breast Disease - - - - Endocrine Breast Diseases - - - - - Pathological processes of the breast. - - - - - - - - breast fibrocystic disease - - - - - - - Adenoses, Microglandular - - - - Adenosis of Breast - - - - Adenosis, Microglandular - - - - Breast Adenosis - - - - Breast Cystic Disease - - - - Breast Cystic Diseases - - - - Breast Disease, Cystic - - - - Breast Disease, Fibrocystic - - - - Breast Dysplasia - - - - Breast Fibrocystic Change - - - - Breast Fibrocystic Changes - - - - Breast Fibrocystic Disease - - - - Chronic Cystic Mastitis - - - - Cystic Breast Disease - - - - Cystic Disease of Breast - - - - Cystic Mastitis, Chronic - - - - Disease, Cystic Breast - - - - Disease, Fibrocystic Breast - - - - Dysplasia, Breast - - - - Dysplasia, Mammary - - - - Fibrocystic Changes of Breast - - - - Fibrocystic Disease of Breast - - - - Fibrocystic Mastopathy - - - - Mammary Dysplasia - - - - Mastopathy, Fibrocystic - - - - Microglandular Adenoses - - - - Microglandular Adenosis - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A common and benign breast disease characterized by varying degree of fibrocystic changes in the breast tissue. There are three major patterns of morphological changes, including fibrosis, formation of cysts, and proliferation of glandular tissue (adenosis). The fibrocystic breast has a dense irregular, lumpy, bumpy consistency. - - - - - - - - mammary cancer - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Breast Benign Neoplasm - - - - Breast Benign Neoplasms - - - - Breast Cancer - - - - Breast Cancers - - - - Breast Neoplasm - - - - Breast Neoplasm, Benign - - - - Breast Neoplasms, Benign - - - - Breast Tumor - - - - Breast Tumors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Neoplasm of the breast. - - - - - - - - ductal breast carcinoma - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Carcinoma, Ductal, Breast - - - - Carcinoma, Infiltrating Duct - - - - Carcinoma, Invasive Ductal, Breast - - - - Carcinoma, Mammary Ductal - - - - Carcinomas, Infiltrating Duct - - - - Carcinomas, Mammary Ductal - - - - Invasive Ductal Carcinoma, Breast - - - - Mammary Ductal Carcinoma - - - - Mammary Ductal Carcinomas - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An invasive (infiltrating) carcinoma of the mammary ductal system (mammary glands) in the human breast. - - - - - - - - inflammatory breast carcinoma - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Inflammatory Breast Cancer (IBC) is a very aggressive type of breast cancer in which the cancer cells block the lymph vessels in the skin of the breast. This type of breast cancer is called “inflammatory” because the breast often looks swollen and red, or “inflamed”, sometimes overnight and can be misdiagnosed as mastitis. Invasion of the local lymphatic ducts impairs drainage and causes edematous swelling of the breast. - - - - - - - - invasive carcinoma of breast - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Metastatic carcinoma of the breast. - - - - - - - - medullary carcinoma - - - - - - - - Medullary carcinoma of the breast is a variant of breast cancer. These tumors have a similar presentation to other breast cancers but are distinguished by a characteristic histologic appearance. In addition, pure medullary carcinomas have a better prognosis than usual cases of infiltrating ductal carcinoma. - - - - - - - - mucinous carcinoma of breast - - Mucinous (colloid) carcinoma is a rare type of invasive breast cancer that is formed when cancer cells within your breast produce mucous. This mucous contains breast cancer cells that are easily distinguished from normal cells under a microscope. Together, the mucous and cancer cells form a jelly-like tumor. Most mucinous carcinomas of the breast are estrogen-receptor positive and HER2/neu negative. This type of breast cancer rarely spreads to your lymph nodes. - - - - - - - - papillary carcinoma of the breast - - Papillary carcinoma is a type of ductal carcinoma in situ (DCIS). This type of breast cancer is rarely invasive, and usually stays within the milk ducts of your breast. Papilla (a projection) refers to the microscopic shape of the cancer cells, which resemble fingers, or threads. - - - - - - - - scirrhous carcinoma of breast - - - - - - - - An infiltrating ductal breast carcinoma associated with stromal fibrosis. - - - - - - - - squamous cell carcinoma of breast - - SCC of the breast was first reported in 1908 by Troell. It is thought to arise directly from the epithelium of the mammary ducts, although an alternate theory is that the tumor arises from foci of squamous metaplasia within a preexisting adenocarcinoma of the breast. Squamous cell carcinoma (SCC) of the breast is rare and generally aggressive. - - - - - - - - tubular carcinoma of breast - - Tubular carcinoma is a rare type of invasive ductal carcinoma of the breast. It takes its name from its microscopic appearance, in which the cancer cells resemble small tubes. Tubular carcinomas tend to be small, estrogen-receptor positive, HER2/neu negative. In some cases, tubular cancer cells are mixed with ductal or lobular cancer cells, giving a mixed-tumor diagnosis. - - - - - - - - invasive lobular carcinoma of breast - - - - - - - - Invasive Lobular Carcinoma (ILC) is a type of breast cancer that starts in the lobules of your breast, where milk is produced. At first, the cancer cells are at work in the lining of the milk lobes, but later these cells invade, or infiltrate, the nearby tissue outside of the lobes. As with invasive ductal carcinoma (IDC), ILC has the potential to spread, or metastasize, to other parts of your body. - - - - - - - - abdominal lymph node - - Within the abdominal cavity, nodes occur in chains along the main branches of the arteries of the intestine and the abdominal aorta. - - - - - - - - anatomical entity - Biological entity, which constitutes the structural organization of a biological organism, or is an attribute of that organization. - - - - - - - - axillary lymph node - - - - - - - - These nodes are in the underarm region and receive lymph from vessels that drain the arm, the walls of the thorax, the breast, and the upper walls of the abdomen. - - - - - - - - cardinal body part - - Anatomical areas of the body. - - - - - - - - brain - - - - - - - - - - - - - Encephalon - - - - Encephalons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The part of Central Nervous System that is contained within the skull (cranium). Arising from the neural tube, the embryonic brain is comprised of three major parts including prosencephalon (the forebrain); mesencephalon (the midbrain); and rhombencephalon (the hindbrain). The developed brain consists of cerebrum; cerebellum; and other structures in the brain stem. - - - - - - - - neuraxis - - - - - - - - - - - - - - - - - - - - The main information-processing organs of the nervous system, consisting of the brain, spinal cord, and meninges. - - - - - - - - chest wall nodule - - - - - - - - Nodules in chest wall - - - - - - - - exocrine gland - - Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands) - - - - - - - - immune system - - The body's defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components. - - - - - - - - inguinal lymph node - - These nodes receive lymph from the legs, the outer portion of the genitalia and the lower abdominal wall. - - - - - - - - lung - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood. - - - - - - - - lymph node - - They are oval or bean shaped bodies (1 - 30 mm in diameter) located along the lymphatic system. - - - - - - - - lymph node of neck - - These nodes are grouped along the lower border of the jaw, in front of and behind the ears, and deep in the neck along the larger blood vessels. They drain the skin of the scalp, face, tissues of the nasal cavity, and the pharynx. - - - - - - - - lymphatic system - - A system of organs and tissues that process and transport immune cells and lymph. - - - - - - - - lymphoid tissue - - - - - - - - - - - - - - - - - - - - - - - - - Lymphatic_Tissue - - - - Lymphatic_Tissues - - - - Lymphoid_Tissues - - - - Tissue,_Lymphatic - - - - Tissue,_Lymphoid - - - - Tissues,_Lymphatic - - - - Tissues,_Lymphoid - - - - - - - - - - - - - - - - - Specialized tissues that are components of the lymphatic system. They provide fixed locations within the body where a variety of lymphocytes can form, mature and multiply. The lymphoid tissues are connected by a network of lymphatic vessels. - - - - - - - - lactiferous gland - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alveoli,_Mammary - - - - Alveolus,_Mammary - - - - Duct,_Mammary - - - - Ducts,_Mammary - - - - Epithelia,_Mammary - - - - Epithelium,_Mammary - - - - Gland,_Mammary - - - - Glands,_Mammary - - - - Mammary_Alveoli - - - - Mammary_Alveolus - - - - Mammary_Duct - - - - Mammary_Ducts - - - - Mammary_Epithelia - - - - Mammary_Epithelium - - - - Mammary_Gland - - - - Mammary_Glands - - - - Mammary_Lobule - - - - Mammary_Lobules - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Glandular tissue in the breast that is under the influence of hormones such as estrogens; progestins; and prolactin. After parturition, the mammary glands secrete milk for the nourishment of the young. - - - - - - - - nervous system - - The entire nerve apparatus, composed of a central part, the brain and spinal cord, and a peripheral part, the cranial and spinal nerves, autonomic ganglia, and plexuses. - - - - - - - - pelvic lymph node - - The nodes here appear mostly along the paths of the blood vessels within the pelvic cavity and receive lymph from the lymphatic vessels in the area. - - - - - - - - respiratory system - - - - - - - - - - - - - Respiratory_Tract - - - - Respiratory_Tracts - - - - - The tubular and cavernous organs and structures, by means of which pulmonary ventilation and gas exchange between ambient air and the blood are brought about. - - - - - - - - thoracic lymph node - - These nodes occur between the lungs and along the windpipe and bronchi, and receive lymph from this area and from the internal wall of the thorax. - - - - - - - - thoracic wall - - The outer margins of the thorax containing skin, deep fascia; thorasic vertebrae; ribs; sternum; and muscles. - - - - - - - - thorax - - - - - Chest - - - The upper part of the trunk between the neck and the abdomen. It contains the chief organs of the circulatory and respiratory systems. - - - - - - - - portion of tissue - - Collections of differentiated cells, such as epithelium; connective tissue; muscles; and nerve tissue. Tissues are cooperatively arranged to form organs with specialized functions such as respiration; digestion; reproduction; movement; and others. - - - - - - - - - Mouse embryo fibroblasts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The 308 cell line is a papilloma-derived keratinocyte cell line from 7,12-dimethylbenz[a]anthracene-treated adult BALB/c mouse skin - - - - - - - - - Mouse 30A5 preadipocytes is a cell line derived from 10Tl 2 fibroblasts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immortalized myeloblast-like cell line originally derived from long-term cultures of murine bone marrow. The most frequently employed subline is 32D clone 3 (32D cl3). - - - - - - - - - Hematopoietic, immature myeloid, nontumorigenic, diploid cell line that is strictly dependent on exogenously supplied interleukin-3 (IL-3) for maintenance of its growth in culture. - - - - - - - - - 3T3-C2 fibroblastic cells, a nondifferentiated subline of 3T3-L1, follow adipogenic process till mitotic clonal expansion stage (2 days after hormonal induction), but do not proceed to terminal differentitation. - - - - - - - - - These cells (often just referred to as F442A cells) are one of several cloned cell lines established from disaggregated Swiss mouse embryos that are capable of differentiating into cells resembling adipocytes. The cells have the morphology of fibroblasts. When the cells reach confluence they spontaneously arrest growth and can be induced to differentiate into white adipocytes in vitro. They also yield a fully differentiated fat pad after subcutaneous injection into nude mice. These cells are used widely as a model system for pre-adypocytes to study the differentiation of adipocytes. - - - - - - - - - - - - - - - - - - - - - - - - - - - L1 is a continuous substrain of 3T3 (Swiss albino) developed through clonal isolation. The cells undergo a pre-adipose to adipose like conversion as they progress from a rapidly dividing to a confluent and contact inhibited state. A high serum content in the medium enhances fat accumulation. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Derived following HIV infection of A3.01. Contains a single integrated copy of defective HIV provirus - - - - - - - - - Derivative of 8E5; retains HIV provirus but does not express HIV proteins. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The A-431 cell line was derived from an epidermoid carcinoma excised from the skin tissue of an 85-year-old female. - - - - - - - - - - - - - - - The A10 cell line was derived from the thoracic aorta of embryonic rat and is a commonly used model of vascular smooth muscle cells (VSMC). - - - - - - - - - - - - - - - - - - - - - - - HAT-sensitive derivative of CEM obtained by treatment with 8-azaguanine. A3.01 is a hypoxanthine/aminopterin/thymidine-sensitive, human immunodeficiency virus-susceptible, human T cell line. - - - - - - - - - - - - - - - - - - - - - This line was cloned by limiting dilution from the A375 melanoma cell line - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The ACH2 cell line is a clonal cell line derived following infection of A3.01 T cells with HIV-1. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT42) transgenic for human TGF alpha. By electron microscopy, these cells exhibit typical hepatocyte features such as peroxisomes and bile canalicular like structure. AML12 cells retain the capacity to express high levels of mRNA for serum (albumin, alpha 1 antitrypsin and transferrin) and gap junction (connexins 26 and 32) proteins, and contain solely isoenzyme 5 of lactate dehydrogenase. - - - - - - - - - - - - - - - Macrophage cell line derived from the bone marrow of C57BL/6 mice - - - - - - - - - - - - - - - - - - - - - AR42J cells derive from azaserine-induced malignant nodules from the rat pancreas. AR42J cells represent the first amphicrine pancreatic cell line with the combined expression of exocrine and neuroendocrine secretory organelles, both of which follow a regulated secretory pathway in response to various secretory stimuli. - - - - - - - - - - - - - - - - - - - - - Human anaplastic thyroid cancer cell line - - - - - - - - - - - - - - - ARPE-19 is a human diploid retinal pigment epithelium (RPE) cell line, which is in many ways similar to RPE in vivo. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An Epstein-Barr virus (EBV)-producer line, designated Akata, was established from a Japanese patient with Burkitt's lymphoma. The Akata line possessed the Burkitt's-type chromosome translocation, t(8q- ; 14q+), and was derived from the tumor cell. Akata cells produced a large quantity of transforming virus upon treatment of cells with anti-immunoglobulin antibodies. Southern blot analysis of viral DNA indicated that the Akata EBV is nondefective and more representative of wild-type viruses. Akata cells should be useful as a source of EBV. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The line was derived from nude mouse xenografts initiated with cells from the ascites of a patient with cancer of the pancreas. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TNF-alpha gene-transduced B78 melanoma cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cell line established from a spontaneous lymphoma obtained from a female BALB/c mouse. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The Ba/F3-mpI cell line was established by introduction of the cDNA encoding the entire cMpI receptor into the IL-3 dependent murine lymphobiastoid cell line Ba/F3. - - - - - - - - - - - - - - - An immortalized murine bone marrow-derived pro-B-cell line. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The CAD cell line is a variant of a CNS-derived Cath.a cell line - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CEM cells are a line of lymphoblastic cells originally derived from a child with acute lymphoblastic leukemia. Like all uncloned cell lines, the original CEM cells are a mixed population of clones with varied genotypes and phenotypes. - - - - - - - - - glucocorticoid resistant clone of CEM - - - - - - - - - - - - - - - - - - - - - - - - - glucocorticoid sensitive clone of CEM - - - - - - - - - - - - - - - - - HAT sensitive derivative of CEM obtained by treatment with 8-azaguanine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP8 cells were isolated from rat brain cortex and immortalized with SV40 large T Ag - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HBE1 cell line is an immortalized line of normal human airway epithelial cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immortalized proximal tubule epithelial cell line from normal adult human kidney. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The HT22 nerve cell line is a subclone of HT4, derived from the mouse hippocampus. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This human stromal cell line was obtained from adherent bone marrow cell layers of Dexter-type long-term BMC (bone marrow culture) after immortalisation with SV40. - - - - - - - - - - - - - - - - - - - - - H4IIEC3 subclone - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RBE4 cells were isolated from rat brain cortex and immortalized with the plasmid pE1A-neo, containing the adenovirus E1A-encoding sequence followed by a neomycin resistance gene. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From 33e412fb08b7c6919543785c94016a1ab0113cfd Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 19:50:45 -0800 Subject: [PATCH 06/17] resoved an issue that caused tests to pass in 4store and fail in AG (non-deterministic) --- test/test_annotator.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_annotator.rb b/test/test_annotator.rb index 3f36f01..e45ac50 100644 --- a/test/test_annotator.rb +++ b/test/test_annotator.rb @@ -242,7 +242,7 @@ def test_annotate annotations = annotator.annotate(text, { ontologies: [], semantic_types: [], - filter_integers: true, + filter_integers: false, expand_class_hierarchy: false, expand_hierarchy_levels: 0, expand_with_mappings: false, @@ -752,7 +752,7 @@ def self.all_classes(ontologies) classes += page_classes end while !page.nil? end - return classes + return classes.sort_by { |c| c.prefLabel } end end From 9cdb46a6b94c1bedb7a4dbab456888459217b7be Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 08:14:11 -0800 Subject: [PATCH 07/17] fixed another failing unit test, test_annotate_minsize_term --- Gemfile.lock | 2 +- test/test_annotator.rb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 902f7c3..4632f19 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: d9aefd5a9bff4fcb40d687b16b25e171457deeeb + revision: 77a98064f91c7cce5d89e31e3b3768dbc9a441a5 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) diff --git a/test/test_annotator.rb b/test/test_annotator.rb index e45ac50..ba1e814 100644 --- a/test/test_annotator.rb +++ b/test/test_annotator.rb @@ -361,7 +361,7 @@ def test_annotate_minsize_term annotations = annotator.annotate(text, { ontologies: [], semantic_types: [], - filter_integers: true, + filter_integers: false, expand_class_hierarchy: false, expand_hierarchy_levels: 0, expand_with_mappings: false, @@ -379,7 +379,7 @@ def test_annotate_minsize_term class_page.each do |cls| if cls.prefLabel.length > 2 #TODO: This assertion may fail if the dictionary file on mgrep server does not contain the terms from the test ontologies - assert_operator 0, :<, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length + assert_operator 0, :<, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length, "expected to find #{cls.id}" found += 1 if cls.prefLabel.length < 10 filter_out_next << cls From 5761522fde315bff8de7d69592d40ad05884d23f Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 12:14:54 -0800 Subject: [PATCH 08/17] config cleanup --- Gemfile.lock | 2 +- Rakefile | 8 -------- docker-compose.yml | 4 ++-- 3 files changed, 3 insertions(+), 11 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 4632f19..76ad3f3 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 77a98064f91c7cce5d89e31e3b3768dbc9a441a5 + revision: 139bb2e327b576c4ec374ad6ceec553cd0de8d11 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) diff --git a/Rakefile b/Rakefile index f40d4cf..764cbc9 100644 --- a/Rakefile +++ b/Rakefile @@ -5,11 +5,3 @@ Rake::TestTask.new do |t| t.warning = false t.test_files = FileList['test/**/test*.rb'] end - -# EX: Adding sub-tasks to rake -# Rake::TestTask.new do |t| -# t.libs = [] -# t.name = "test:models" -# t.test_files = FileList['test/models/test*.rb'] -# end - diff --git a/docker-compose.yml b/docker-compose.yml index 43f565f..204b539 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -10,8 +10,8 @@ x-app: &app REDIS_PORT: 6379 MGREP_HOST: mgrep-ut MGREP_PORT: 55556 - SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr/term_search_core1 - SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1 + SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr + SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr volumes: - .:/app - bundle:/usr/local/bundle From 30ae1929a038650fb5685b075d960ff8a4a96dba Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 12:17:10 -0800 Subject: [PATCH 09/17] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 76ad3f3..2c69b79 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -104,7 +104,7 @@ GEM i18n (1.14.8) concurrent-ruby (~> 1.0) io-console (0.8.2) - json (2.18.0) + json (2.18.1) libxml-ruby (5.0.5) link_header (0.0.8) logger (1.7.0) @@ -295,7 +295,7 @@ CHECKSUMS http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc - json (2.18.0) sha256=b10506aee4183f5cf49e0efc48073d7b75843ce3782c68dbeb763351c08fd505 + json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a link_header (0.0.8) sha256=15c65ce43b29f739b30d05e5f25c22c23797e89cf6f905dbb595fb4c70cb55f9 logger (1.7.0) sha256=196edec7cc44b66cfb40f9755ce11b392f21f7967696af15d274dde7edff0203 From 24816f09b2e8b9326f0009f6452dcdbc9c6d60e8 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 22:25:58 -0800 Subject: [PATCH 10/17] moved settings override in config to the bottom, so override can work --- Gemfile.lock | 2 +- lib/ncbo_annotator/config.rb | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 2c69b79..b08f36a 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 139bb2e327b576c4ec374ad6ceec553cd0de8d11 + revision: 9282060c02a6ca242d9c4652e3f66799d3475d43 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) diff --git a/lib/ncbo_annotator/config.rb b/lib/ncbo_annotator/config.rb index a2ed17c..41d09e4 100644 --- a/lib/ncbo_annotator/config.rb +++ b/lib/ncbo_annotator/config.rb @@ -11,9 +11,6 @@ module Annotator def config(&block) return if @settings_run - @settings_run = true - - yield @settings if block_given? # Set defaults @settings.goo_port ||= 9000 @@ -43,6 +40,9 @@ def config(&block) @settings.annotator_redis_prefix ||= "c1:" @settings.annotator_redis_alt_prefix ||= "c2:" + + yield @settings if block_given? + @settings_run = true end end From 78f53234d52f4938047972425d1cc58933882f86 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 22:47:41 -0800 Subject: [PATCH 11/17] Gemfile.lock update --- Gemfile.lock | 6 +++--- test/test_case.rb | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index b08f36a..e7fbc9d 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 9282060c02a6ca242d9c4652e3f66799d3475d43 + revision: abb93105158193d348daba0e1b0e005174e14061 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) @@ -120,7 +120,7 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0127) + mime-types-data (3.2026.0203) mini_mime (1.1.5) minitest (6.0.1) prism (~> 1.5) @@ -303,7 +303,7 @@ CHECKSUMS mail (2.9.0) sha256=6fa6673ecd71c60c2d996260f9ee3dd387d4673b8169b502134659ece6d34941 method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2026.0127) sha256=4a58692436a987ad930e75bf8f24da7e627acfa0d06e1720aa514791b4c7d12b + mime-types-data (3.2026.0203) sha256=54353d693af028847391c28361c07d4b8b689cad78c3e1cc272fb1205c6d2a2f mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef minitest (6.0.1) sha256=7854c74f48e2e975969062833adc4013f249a4b212f5e7b9d5c040bf838d54bb minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c diff --git a/test/test_case.rb b/test/test_case.rb index 1f65234..443693d 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -15,7 +15,6 @@ end end -require 'ontologies_linked_data' require_relative '../lib/ncbo_annotator' require_relative '../config/config' From e4be8480530700a6a1bd165b03cc6a331a029077 Mon Sep 17 00:00:00 2001 From: = Date: Thu, 5 Feb 2026 15:25:21 -0800 Subject: [PATCH 12/17] updated search servers in docker-compose --- Gemfile.lock | 4 ++-- docker-compose.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index e7fbc9d..202191f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d + revision: 13a8559a2346cc8320d7d36046646907bfa8a27c branch: ontoportal-lirmm-development specs: goo (0.0.2) @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: abb93105158193d348daba0e1b0e005174e14061 + revision: b731028f1a6781ff2254238486c5b057c39f4596 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) diff --git a/docker-compose.yml b/docker-compose.yml index 204b539..c643b99 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -3,7 +3,7 @@ x-app: &app build: context: . args: - RUBY_VERSION: '3.1' + RUBY_VERSION: '3.2' environment: &env COVERAGE: 'true' # enable simplecov code coverage REDIS_HOST: redis-ut From e86ece03c2d80604cdea4d96bd1de6899f6b4762 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 12:58:41 -0800 Subject: [PATCH 13/17] added support for json/ld --- Gemfile | 2 ++ Gemfile.lock | 26 +++++++++++++++++++++----- 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/Gemfile b/Gemfile index 74549b7..9be1a91 100644 --- a/Gemfile +++ b/Gemfile @@ -6,6 +6,8 @@ gem 'oj', '~> 3.0' gem 'rake' gem 'request_store' gem 'parallel' +gem 'json-ld' +gem 'jwt' gem 'ruby-xxHash' gem 'activesupport' diff --git a/Gemfile.lock b/Gemfile.lock index 202191f..c28ad4b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -18,7 +18,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: b731028f1a6781ff2254238486c5b057c39f4596 + revision: 3204c0a830d344eb9ae1db82c22b46be1ef468b3 branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) @@ -80,7 +80,7 @@ GEM down (5.4.2) addressable (~> 2.8) drb (2.2.3) - faraday (2.14.0) + faraday (2.14.1) faraday-net_http (>= 2.0, < 3.5) json logger @@ -105,6 +105,17 @@ GEM concurrent-ruby (~> 1.0) io-console (0.8.2) json (2.18.1) + json-canonicalization (1.0.0) + json-ld (3.3.2) + htmlentities (~> 4.3) + json-canonicalization (~> 1.0) + link_header (~> 0.0, >= 0.0.8) + multi_json (~> 1.15) + rack (>= 2.2, < 4) + rdf (~> 3.3) + rexml (~> 3.2) + jwt (3.1.2) + base64 libxml-ruby (5.0.5) link_header (0.0.8) logger (1.7.0) @@ -147,7 +158,7 @@ GEM net-smtp (0.5.1) net-protocol netrc (0.11.0) - oj (3.16.13) + oj (3.16.15) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -246,6 +257,8 @@ DEPENDENCIES faraday ffi goo! + json-ld + jwt minitest minitest-reporters oj (~> 3.0) @@ -276,7 +289,7 @@ CHECKSUMS domain_name (0.6.20240107) sha256=5f693b2215708476517479bf2b3802e49068ad82167bcd2286f899536a17d933 down (5.4.2) sha256=516e5e01e7a96214a7e2cd155aac6f700593038ae6c857c0f4a05413b1c58acf drb (2.2.3) sha256=0b00d6fdb50995fe4a45dea13663493c841112e4068656854646f418fda13373 - faraday (2.14.0) sha256=8699cfe5d97e55268f2596f9a9d5a43736808a943714e3d9a53e6110593941cd + faraday (2.14.1) sha256=a43cceedc1e39d188f4d2cdd360a8aaa6a11da0c407052e426ba8d3fb42ef61c faraday-net_http (3.4.2) sha256=f147758260d3526939bf57ecf911682f94926a3666502e24c69992765875906c ffi (1.17.3) sha256=0e9f39f7bb3934f77ad6feab49662be77e87eedcdeb2a3f5c0234c2938563d4c ffi (1.17.3-aarch64-linux-gnu) sha256=28ad573df26560f0aedd8a90c3371279a0b2bd0b4e834b16a2baa10bd7a97068 @@ -296,6 +309,9 @@ CHECKSUMS i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 + json-canonicalization (1.0.0) sha256=d4848a8cca7534455c6721f2d9fc9e5e9adca49486864a898810024f67d59446 + json-ld (3.3.2) sha256=b9531893bf5bdc01db428e96953845a23adb1097125ce918ae0f97c4a6e1ab27 + jwt (3.1.2) sha256=af6991f19a6bb4060d618d9add7a66f0eeb005ac0bc017cd01f63b42e122d535 libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a link_header (0.0.8) sha256=15c65ce43b29f739b30d05e5f25c22c23797e89cf6f905dbb595fb4c70cb55f9 logger (1.7.0) sha256=196edec7cc44b66cfb40f9755ce11b392f21f7967696af15d274dde7edff0203 @@ -316,7 +332,7 @@ CHECKSUMS net-protocol (0.2.2) sha256=aa73e0cba6a125369de9837b8d8ef82a61849360eba0521900e2c3713aa162a8 net-smtp (0.5.1) sha256=ed96a0af63c524fceb4b29b0d352195c30d82dd916a42f03c62a3a70e5b70736 netrc (0.11.0) sha256=de1ce33da8c99ab1d97871726cba75151113f117146becbe45aa85cb3dabee3f - oj (3.16.13) sha256=b114bcb83ef884f1736b3112108f77cf9ca90aa8111a775318cc5d7a6a1e0303 + oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e ontologies_linked_data (0.0.1) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 From cd45ea2d2a19cda8b9cab17fe27ecf841860cba3 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 3 Mar 2026 15:04:52 -0800 Subject: [PATCH 14/17] integrate ontoportal testkit --- .github/workflows/ruby-unit-tests.yml | 32 --------- .github/workflows/testkit-unit-tests.yml | 87 ++++++++++++++++++++++++ .ontoportal-testkit.yml | 9 +++ Dockerfile | 28 ++------ Gemfile | 1 + Gemfile.lock | 10 +++ config/config.test.rb | 24 ++++--- rakelib/ontoportal_testkit.rake | 2 + test/test_case.rb | 4 +- test/test_mgrep_client.rb | 5 +- 10 files changed, 130 insertions(+), 72 deletions(-) delete mode 100644 .github/workflows/ruby-unit-tests.yml create mode 100644 .github/workflows/testkit-unit-tests.yml create mode 100644 .ontoportal-testkit.yml create mode 100644 rakelib/ontoportal_testkit.rake diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml deleted file mode 100644 index f2d562b..0000000 --- a/.github/workflows/ruby-unit-tests.yml +++ /dev/null @@ -1,32 +0,0 @@ -name: Ruby Unit Tests - -on: - push: - pull_request: - -jobs: - test: - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - backend: ['ruby', 'ruby-agraph'] # api runs tests with 4store backend and api-agraph runs with AllegroGraph backend - steps: - - uses: actions/checkout@v4 - - name: copy config file - run: cp config/config.test.rb config/config.rb - - name: Build docker compose - run: docker compose build - - name: Run unit tests - # unit tests are run inside a container - # http://docs.codecov.io/docs/testing-with-docker - run: | - ci_env=`bash <(curl -s https://codecov.io/env)` - docker compose run $ci_env -e CI ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v' - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v5 - with: - token: ${{ secrets.CODECOV_TOKEN }} - flags: unittests - verbose: true - fail_ci_if_error: false # optional (default = false) diff --git a/.github/workflows/testkit-unit-tests.yml b/.github/workflows/testkit-unit-tests.yml new file mode 100644 index 0000000..d763837 --- /dev/null +++ b/.github/workflows/testkit-unit-tests.yml @@ -0,0 +1,87 @@ +name: Docker Unit Tests + +on: + push: + branches: + - '**' + tags-ignore: + - '**' + pull_request: + +env: + # CI execution mode for backend tests: + # - container: run `test:docker::container` (default) + # - native: run `test:docker:` on host Ruby + # OPTK_CI_RUN_MODE: ${{ vars.OPTK_CI_RUN_MODE || 'container' }} + # Example override to force native mode in this workflow file: + OPTK_CI_RUN_MODE: native + +jobs: + prepare: + runs-on: ubuntu-latest + outputs: + backends: ${{ steps.cfg.outputs.backends }} + steps: + - uses: actions/checkout@v4 + + - id: cfg + name: Read backend matrix from .ontoportal-testkit.yml + run: | + BACKENDS=$(ruby -ryaml -rjson -e 'c=YAML.safe_load_file(".ontoportal-testkit.yml") || {}; b=c["backends"] || %w[fs ag vo gd]; puts JSON.generate(b)') + echo "backends=$BACKENDS" >> "$GITHUB_OUTPUT" + + test: + needs: prepare + runs-on: ubuntu-latest + timeout-minutes: 45 + strategy: + fail-fast: false + matrix: + backend: ${{ fromJson(needs.prepare.outputs.backends) }} + + steps: + - uses: actions/checkout@v4 + + - name: Set up Ruby from .ruby-version + uses: ruby/setup-ruby@v1 + with: + ruby-version: .ruby-version + bundler-cache: true + + - name: Set up Java 11 (native mode) + if: env.OPTK_CI_RUN_MODE == 'native' + uses: actions/setup-java@v4 + with: + distribution: temurin + java-version: '11' + + - name: Install native system dependencies + if: env.OPTK_CI_RUN_MODE == 'native' + run: | + sudo apt-get update + sudo apt-get install -y raptor2-utils + + - name: Run unit tests + env: + CI: "true" + TESTOPTS: "-v" + BACKEND: ${{ matrix.backend }} + run: | + MODE="${OPTK_CI_RUN_MODE:-container}" + TASK="test:docker:${BACKEND}" + if [ "$MODE" = "container" ]; then + TASK="${TASK}:container" + elif [ "$MODE" != "native" ]; then + echo "Invalid OPTK_CI_RUN_MODE=$MODE (expected container or native)" + exit 1 + fi + + bundle exec rake "$TASK" + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v5 + with: + token: ${{ secrets.CODECOV_TOKEN }} + flags: unittests,${{ matrix.backend }} + verbose: true + fail_ci_if_error: false diff --git a/.ontoportal-testkit.yml b/.ontoportal-testkit.yml new file mode 100644 index 0000000..161f930 --- /dev/null +++ b/.ontoportal-testkit.yml @@ -0,0 +1,9 @@ +component_name: ncbo_annotator +app_service: test-container +backends: + - fs + - ag + - vo + - gd +dependency_services: + - mgrep diff --git a/Dockerfile b/Dockerfile index c585383..6c56623 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,38 +1,18 @@ -ARG RUBY_VERSION=3.1 +ARG RUBY_VERSION=3.2 ARG DISTRO=bullseye - -FROM ruby:$RUBY_VERSION-$DISTRO - -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential \ - git \ - libxml2 \ - libxslt-dev \ - openjdk-11-jre-headless \ - raptor2-utils \ - && rm -rf /var/lib/apt/lists/* +ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO} +FROM ${TESTKIT_BASE_IMAGE} WORKDIR /app -# Use a dedicated bundle path -ENV BUNDLE_PATH=/usr/local/bundle -ENV GEM_HOME=/usr/local/bundle -ENV PATH="$BUNDLE_PATH/bin:$PATH" - COPY Gemfile* *.gemspec ./ -RUN gem update --system - -#I nstall the exact Bundler version from Gemfile.lock (if it exists) +# Respect the project's Bundler lock when present. RUN if [ -f Gemfile.lock ]; then \ BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \ gem install bundler -v "$BUNDLER_VERSION"; \ - else \ - gem install bundler; \ fi -RUN bundle config set --local path '/usr/local/bundle' -RUN bundle config set --global no-document 'true' RUN bundle install --jobs 4 --retry 3 COPY . ./ diff --git a/Gemfile b/Gemfile index 9be1a91..ac829ed 100644 --- a/Gemfile +++ b/Gemfile @@ -14,6 +14,7 @@ gem 'activesupport' group :test do gem 'minitest' gem 'minitest-reporters' + gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main' gem 'pry' gem 'simplecov' gem 'simplecov-cobertura' # for codecov.io diff --git a/Gemfile.lock b/Gemfile.lock index c28ad4b..e037eaf 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,3 +1,11 @@ +GIT + remote: https://github.com/alexskr/ontoportal_testkit.git + revision: 741b25d35ed3e3bdbdcbc55f4672a5258215ecdb + branch: main + specs: + ontoportal_testkit (0.1.0) + rake (>= 13.0) + GIT remote: https://github.com/ncbo/goo.git revision: 13a8559a2346cc8320d7d36046646907bfa8a27c @@ -263,6 +271,7 @@ DEPENDENCIES minitest-reporters oj (~> 3.0) ontologies_linked_data! + ontoportal_testkit! parallel pry rake @@ -335,6 +344,7 @@ CHECKSUMS oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e ontologies_linked_data (0.0.1) + ontoportal_testkit (0.1.0) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7 diff --git a/config/config.test.rb b/config/config.test.rb index c33e281..afdfa2c 100644 --- a/config/config.test.rb +++ b/config/config.test.rb @@ -16,21 +16,23 @@ SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" - LinkedData.config do |config| - config.goo_backend_name = GOO_BACKEND_NAME.to_s - config.goo_host = GOO_HOST.to_s - config.goo_port = GOO_PORT.to_i - config.goo_path_query = GOO_PATH_QUERY.to_s - config.goo_path_data = GOO_PATH_DATA.to_s - config.goo_path_update = GOO_PATH_UPDATE.to_s - config.search_server_url = SOLR_TERM_SEARCH_URL.to_s - config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s + config.goo_backend_name = GOO_BACKEND_NAME.to_s + config.goo_host = GOO_HOST.to_s + config.goo_port = GOO_PORT.to_s + config.goo_path_query = GOO_PATH_QUERY.to_s + config.goo_path_data = GOO_PATH_DATA.to_s + config.goo_path_update = GOO_PATH_UPDATE.to_s + config.search_server_url = SOLR_TERM_SEARCH_URL.to_s + config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s end + Annotator.config do |config| config.mgrep_host = MGREP_HOST.to_s - config.mgrep_port = MGREP_PORT.to_i + config.mgrep_port = MGREP_PORT.to_s + config.mgrep_alt_host = MGREP_HOST.to_s + config.mgrep_alt_port = MGREP_PORT.to_s config.mgrep_dictionary_file = './test/data/dictionary.txt' config.annotator_redis_host = REDIS_HOST.to_s - config.annotator_redis_port = REDIS_PORT.to_i + config.annotator_redis_port = REDIS_PORT.to_s end diff --git a/rakelib/ontoportal_testkit.rake b/rakelib/ontoportal_testkit.rake new file mode 100644 index 0000000..7f04305 --- /dev/null +++ b/rakelib/ontoportal_testkit.rake @@ -0,0 +1,2 @@ +# Loads shared OntoPortal testkit rake tasks into this component. +require "ontoportal/testkit/tasks" diff --git a/test/test_case.rb b/test/test_case.rb index 443693d..e638438 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -16,10 +16,10 @@ end require_relative '../lib/ncbo_annotator' -require_relative '../config/config' +require_relative '../config/config.test' # Check to make sure you want to run if not pointed at localhost -safe_host = Regexp.new(/localhost|-ut|ncbo-dev*|ncbo-unittest*/) +safe_host = Regexp.new(/localhost|-ut*/) unless LinkedData.settings.goo_host.match(safe_host) && LinkedData.settings.search_server_url.match(safe_host) && Annotator.settings.annotator_redis_host.match(safe_host) print '\n\n================================== WARNING ==================================\n' print '** TESTS CAN BE DESTRUCTIVE -- YOU ARE POINTING TO A POTENTIAL PRODUCTION/STAGE SERVER **\n' diff --git a/test/test_mgrep_client.rb b/test/test_mgrep_client.rb index 7a70ca6..0369abe 100644 --- a/test/test_mgrep_client.rb +++ b/test/test_mgrep_client.rb @@ -1,8 +1,7 @@ -require "pry" require "minitest/autorun" -require_relative "../lib/ncbo_annotator.rb" -require_relative "../config/config.rb" +require_relative "../lib/ncbo_annotator" +require_relative "../config/config.test" class TestMgrepClient < Minitest::Test From 6c309069600da210d5d8f30204ca7c78a91cbce2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 3 Mar 2026 15:09:33 -0800 Subject: [PATCH 15/17] clean up --- .ruby-version | 2 +- docker-compose.yml | 121 --------------------------------------------- run-unit-tests.sh | 10 ---- 3 files changed, 1 insertion(+), 132 deletions(-) delete mode 100644 docker-compose.yml delete mode 100755 run-unit-tests.sh diff --git a/.ruby-version b/.ruby-version index be94e6f..f15386a 100644 --- a/.ruby-version +++ b/.ruby-version @@ -1 +1 @@ -3.2.2 +3.2.10 diff --git a/docker-compose.yml b/docker-compose.yml deleted file mode 100644 index c643b99..0000000 --- a/docker-compose.yml +++ /dev/null @@ -1,121 +0,0 @@ -x-app: &app - image: ncbo_annotator:0.0.3 - build: - context: . - args: - RUBY_VERSION: '3.2' - environment: &env - COVERAGE: 'true' # enable simplecov code coverage - REDIS_HOST: redis-ut - REDIS_PORT: 6379 - MGREP_HOST: mgrep-ut - MGREP_PORT: 55556 - SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr - SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr - volumes: - - .:/app - - bundle:/usr/local/bundle - stdin_open: true - tty: true - command: "bundle exec rake test TESTOPTS='-v'" - depends_on: &depends_on - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - mgrep-ut: - condition: service_healthy - -services: - ruby: - <<: *app - environment: - <<: *env - GOO_BACKEND_NAME: 4store - GOO_PORT: 9000 - GOO_HOST: 4store-ut - depends_on: - <<: *depends_on - 4store-ut: - condition: service_started - profiles: - - 4store - - ruby-agraph: - <<: *app - environment: - <<: *env - GOO_BACKEND_NAME: ag - GOO_PORT: 10035 - GOO_HOST: agraph-ut - GOO_PATH_QUERY: /repositories/ontoportal_test - GOO_PATH_DATA: /repositories/ontoportal_test/statements - GOO_PATH_UPDATE: /repositories/ontoportal_test/statements - depends_on: - <<: *depends_on - agraph-ut: - condition: service_healthy - profiles: - - agraph - - solr-ut: - image: ontoportal/solr-ut:0.2.0 - healthcheck: - test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"] - start_period: 3s - interval: 10s - timeout: 5s - retries: 5 - - redis-ut: - image: redis - healthcheck: - test: redis-cli ping - interval: 10s - timeout: 3s - retries: 10 - - mgrep-ut: - image: ontoportal/mgrep:0.0.3 - platform: linux/amd64 - healthcheck: - test: ["CMD", "nc", "-z", "-v", "127.0.0.1", "55556"] - start_period: 3s - interval: 10s - timeout: 5s - retries: 5 - - 4store-ut: - image: bde2020/4store - platform: linux/amd64 - command: > - bash -c "4s-backend-setup --segments 4 ontoportal_kb - && 4s-backend ontoportal_kb - && 4s-httpd -D -s-1 -p 9000 ontoportal_kb" - profiles: - - 4store - - agraph-ut: - image: franzinc/agraph:v8.3.1 - platform: linux/amd64 - environment: - - AGRAPH_SUPER_USER=test - - AGRAPH_SUPER_PASSWORD=xyzzy - shm_size: 1g - command: > - bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start - ; agtool repos create --supersede ontoportal_test - ; agtool users add anonymous - ; agtool users grant anonymous root:ontoportal_test:rw - ; tail -f /agraph/data/agraph.log" - healthcheck: - test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"] - start_period: 30s - interval: 10s - timeout: 5s - retries: 5 - profiles: - - agraph - -volumes: - bundle: diff --git a/run-unit-tests.sh b/run-unit-tests.sh deleted file mode 100755 index e25a7a8..0000000 --- a/run-unit-tests.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -# sample script for running unit tests in docker. This functionality should be moved to a rake task -# -# add config for unit testing -[ -f config/config.rb ] || cp config/config.test.rb config/config.rb -docker-compose build - -docker compose run --rm ruby bundle exec rake test TESTOPTS='-v' -#docker compose run --rm ruby-agraph bundle exec rake test TESTOPTS='-v' -docker compose --profile agraph --profile 4store stop From f760776d328eb44292d0fc2c8e3f42d758a923c4 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 6 Mar 2026 12:40:23 -0800 Subject: [PATCH 16/17] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index e037eaf..8af47ee 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/alexskr/ontoportal_testkit.git - revision: 741b25d35ed3e3bdbdcbc55f4672a5258215ecdb + revision: 5138aa94c028ec97adeaf1f7a5ed9f1c40b12950 branch: main specs: ontoportal_testkit (0.1.0) @@ -384,4 +384,4 @@ CHECKSUMS uuid (2.3.9) sha256=aec0cf592053cd6e07c13c1ef94c440aba705f22eb1ee767b39631f2760124d7 BUNDLED WITH - 4.0.5 + 4.0.7 From 2b4efe17a95b5be42ead4d4507c50c244ef24e0f Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Thu, 19 Mar 2026 14:11:17 -0700 Subject: [PATCH 17/17] Gemfile.lock update --- Gemfile | 4 ++-- Gemfile.lock | 10 +++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/Gemfile b/Gemfile index ac829ed..512b628 100644 --- a/Gemfile +++ b/Gemfile @@ -21,6 +21,6 @@ group :test do end # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'goo', github: 'ncbo/goo', branch: 'ontoportal-lirmm-development' +gem 'goo', github: 'ncbo/goo', branch: 'main' gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'chore/ontoportal-lirmm-goo-compat' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'main' diff --git a/Gemfile.lock b/Gemfile.lock index 8af47ee..54e0c11 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -8,8 +8,8 @@ GIT GIT remote: https://github.com/ncbo/goo.git - revision: 13a8559a2346cc8320d7d36046646907bfa8a27c - branch: ontoportal-lirmm-development + revision: 2411deb0143c773b9e6d89b3232c9cca0d50e2bd + branch: main specs: goo (0.0.2) addressable (~> 2.8) @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 3204c0a830d344eb9ae1db82c22b46be1ef468b3 + revision: e7310135a510369384204d873ba8b1c5039fcdbc branch: chore/ontoportal-lirmm-goo-compat specs: ontologies_linked_data (0.0.1) @@ -48,8 +48,8 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 - branch: ontoportal-lirmm-development + revision: fa69937120104bafb3d3b8350e4f2df2efb7c247 + branch: main specs: sparql-client (3.2.2) net-http-persistent (~> 4.0, >= 4.0.2)