wormbase.conf

######################################################
#
#  WormBase Default Configuration
#
#  This file contains defaults for the WormBase application.
#  It should not be edited.  Should you wish to over-ride any
#  variables, provide them in a local configuration file
#  according to the following rules.
#
#  Configuration file precedence (highest to lowest)
#
#  1. Via environment variable provided on the command line
#     or in the script/wormbase-init.sh script. For example, the following
#     command will load $approot/wormbase_staging.conf with the highest
#     precedence.
#
#     CATALYST_CONFIG_LOCAL_SUFFIX=staging ./script/wormbase_server.pl -p 8000
#
#  2. Alternatively, provide a local configuration file
#     $approot/wormbase_local.conf
#
#  3. This file:
#     $approot/wormbase.conf
#
######################################################


######################################################
#
#   General
#
######################################################
site_name   = WormBase
site_byline = Nematode Information Resource

# Are we a (development|mirror|local|production) site?
# Used to determine whcih javascript to use.
installation_type   = development

# Version information
version      = 0.02
perl_version = 5.010000
codename     = Saag Paneer

# For providing Google maps on strain pages
google_api_key      = ABQIAAAAX6AZGEUlM28m4mzs0PsGkhRVfLFVmRFz44kSxZwC_XT2TLrxixTVyjZlGBxla25vFXfsh17xrvYj0g

# These all need to be reset and moved outside of version control
facebook_secret_key  = a7c919f6d562e140cb6baebe8c7e4a80
facebook_app_id      = 145770318837275
twitter_consumer_key = dORNthy42qJmltFfBEplQ
twitter_consumer_secret  = ZT89nA5lmc3hGSre14dHSGCcciEPFpOWwCabaM8VUE

# Datomic to catayl location
# rest_server = "http://rest-dev.wormbase.org" # alias for stable development instance
# rest_server = "http://10.0.0.243:3000" # stable development instance (AWS private IP)
# rest_server = "http://54.152.75.107:3000" # stable development instance (AWS public IP)
# rest_server = "http://rest.wormbase.org" # production instance
rest_server = "http://wormbase-rest-ws277.us-east-1.elasticbeanstalk.com" # production instance (probably over AWS public IP) # this value can be overriden in the wormbase_staging.conf

# new search API endpoint
search_server = "http://wormbase-search-ws277.us-east-1.elasticbeanstalk.com"
# max ratio of traffic to divert to new search API (the remainig will go to Xapian)
max_ratio_elasticsearch_traffic = 0.3 # maybe overwritten in wormbase_staging.conf

# cached_rest_endpoints_expires_in = 20160 # minutes, for pre-caching
cached_rest_endpoints_expires_in = 5 # minutes, for production
precache_mode = 0  # turn this on during pre-caching step only

#intermine
intermine_server = "http://intermine.wormbase.org"

# This is the site-wide (dismissable) system message.
# The id is used to make sure a new message won't be hidden
<system_message>
    message = "Welcome to WormBase - <a target=\"_blank\" href=\"/tools/support\">need help</a>?"
    id = 6
</system_message>

survey_link = "http://www.wormbase.org"

# enable_ssl = 1;
#       secure_uri_for will return the uri with the scheme https
# enable_ssl = 0;
#       secure_uri_for will return the results of uri_for
enable_ssl = 0

# Are we using a front end proxy in front of our server?
# At WormBase, typically we are (except when running the Catalyst server itself)
using_frontend_proxy = 1

# BASE URL: Not required for default installations
# base = http://www.wormbase.org/

# For posting issues to github -
github_repo = "wormbase/website"
github_api_base = "http://upstream-proxy:3001"  # go through the proxy via http, due to intermittent failure with https in starman running inside docker container

# uncomment this to activate WormMine
# Note: This will break log in functionality if WormMine is not running at this path:
wormmine_path = "tools/wormmine"

wormbase_release = "WS277"
parasite_release = "WBPS11"  #override in lib/WormBase/Web.pm

shared_content_dir = "/usr/local/wormbase/website-shared-files/html"



######################################################
#
#   Debugging
#
######################################################

# debug: enable system-wide debugging; expects boolean
debug = 0
# debug_view: style of the view debugging. Off by default
#    unless "debug" is set above and debug_view set to
#    one of
#     comment - send debugging statements as HTML comments
#     browser - send debugging statements in formatted divs
#     log     - send to the error log file
debug_view =

# Enable fatal data stucture compliance. Rendering of
# widgets will fail if this is set to a true value.
fatal_non_compliance = 0


######################################################
#
#   User Interface
#
######################################################

#  Widget timing information.
#  Enable display of timing, back end server,
#  and cache information. You must also be an
#  administrator. Uncommenting disables BOTH
#  the collection and display of this information.
timer = 0

# Configuration of R visualization (barcharts, boxplots, other charts)

# FPKM Expression Chart (Gene page, Expression widget)
fpkm_expression_chart_xlabel = Measurement
fpkm_expression_chart_ylabel = FPKM
fpkm_expression_chart_width  = 1280
fpkm_expression_chart_height = 1900
fpkm_expression_chart_height_shorter_if_less_than_X_facets = 4
fpkm_expression_chart_rotate = 1
fpkm_expression_chart_bw     = 1
fpkm_expression_chart_facets = 1

########################################################
#
#  FILE PATHS
#
########################################################

gbrowse_conf_dir = __path_to(conf)__/gbrowse
tmp_img_base     = /tmp

# Where static movies live on the file system
static_movie_base = http://www.wormbase.org/img-static/movies/

# Where static images (such as the expression renders) live on the file system
# Note: This path served by Static::Simple as specified in Web.pm.
shared_html_base  = /usr/local/wormbase/website-shared-files/html

# image_base_classic = /usr/local/wormbase/website-shared-files/html/images-website-classic


########################################################
#
#  Cache
#
########################################################

<cache>
    enabled 0
    default couchdb

    <couchdb>
       enabled 0
       # server 127.0.0.1:5984 # defaults
       # The production couchdb is located at
       # server couchdb.wormbase.org:443  # defaults
       # Set this in your wormbase_local.conf if you'd like to use it.
       # Note that you MUST specify the port even though it's on 80.
    </couchdb>

    <memcached>
       enabled 0 # not used in code right now
       expires 4 weeks
       server 206.108.125.168:11211
       server 206.108.125.175:11211
       server 206.108.125.177:11211
       server 206.108.125.178:11211
       server 206.108.125.190:11211
    </memcached>

    <filecache>
       enabled 0
       root __path_to(root)__/tmp/cache
    </filecache>
</cache>

########################################################
#
#  EMAILS
#
########################################################

# Issue tracking and reporting
issue_email = help@wormbase.org

# Registering a new account
register_email = oicr@wormbase.org

# For sending emails
no_reply = no-reply@wormbase.org


########################################################
#
#  GBrowse
#
########################################################

# Sets a redirect within Catalyst to GBrowse. Also needs
# the "genome" tool uncommented below.
#
# For example, when you want to redirect
#     http://dev.wormbase.org:4455/tools/genome/gbrowse/c_elegans
# to
#     http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse/c_elegans
# then set
#     gbrowse_base_uri = http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse
#
# No trailing "/" character permitted.
gbrowse_base_uri = http://dev.wormbase.org:10006/tools/genome/gbrowse

<WormBase::Web::Controller::GBrowse>
        cgi_root_path    test
        cgi_dir          cgi-bin/gb2
#        cgi_chain_root   /optional/private/path/to/Chained/root
#        cgi_file_pattern *
        # or regex
        cgi_file_pattern /gbrowse/
        <CGI>
#            username_field username # used for REMOTE_USER env var
            pass_env PERL5LIB
            pass_env PATH
            pass_env /^WORMBASE_/
        pass_env GB_HOME
#       pass_env GBROWSE_CONF
        </CGI>
</WormBase::Web::Controller::GBrowse>


########################################################
#
#  API & REST CONFIGURATION
#  Should probably be Controller::REST
#
########################################################
<api>
      <content_type>
         application/json = json
         text/xml         = xml
         text/x-yaml      = yml
         text/html        = html
         text/csv         = csv
      </content_type>
</api>


########################################################
# Authentication&Authorization: Configuration in Web.pm
########################################################
#<authentication>
#  default_realm = members
#  <realms>
#    <members>
#        <credential>
#   </credential>
#   <store>
#     class = DBIx::Class
#     user_model = Schema::User
#     role_relation = roles
#     role_field = role
#     #ignore_fields_in_find = remote_name
#     #use_userdata_from_session = 1,
#   </store>
#    </members>
#    <openid>
#      <credential>
#   class = OpenID
#   ua_class = LWP::UserAgent
#   <extensions>
#           http://openid.net/extensions/sreg/1.1
#           required =  email
#      optional =  fullname nickname timezone
#        </extensions>
#      </credential>
#    </openid>
#  </realms>
#</authentication>

<Model::Schema>
  schema_class = WormBase::Schema
  <connect_info>
 #       dsn =  dbi:mysql:wormbase_user:hostname=localhost
 #       user = wormbase
 #       password =
        # You can find production here although you won't
    # be able to access it unless specifically granted
    # permissions.
         dsn =  dbi:mysql:wormbase_user:hostname=mysql.wormbase.org
         user = wormbase
         password = sea3l3ganz
   </connect_info>
</Model::Schema>

password_reset_expires = 86400  # 24 hours

<Model::Mendeley>
       <args>
          consumer_key      = f67b2a45de14e07cc9658f779dd22a5804d32335b
      consumer_secret   = 1bd1255a50325e72840d33ae8decac11
      authorization_url = http://api.mendeley.com/oauth/authorize/
      request_token_url = http://api.mendeley.com/oauth/request_token/
      access_token_url  = http://api.mendeley.com/oauth/access_token/
    </args>
</Model::Mendeley>


########################################################
#
#  Database Locations and Authorization
#
#  By default, we use remote data sources for
#  convenience but expect this to be overriden
#  by the wormbase_local.conf.
#
########################################################
<Model::WormBaseAPI>
    class = WormBase::API
    <args>
        <pre_compile>
            base =  /usr/local/wormbase/databases
            gene = /gene
            position_matrix = /position_matrix

        # These are all old precompiled files from CompileGeneResources. None are
        # in use any longer
            # rnai_details_file =  rnai_data.txt
            # gene_rnai_phene_file =  gene_rnai_pheno.txt
            # gene_variation_phene_file =  variation_data.txt
            # phenotype_name_file =  phenotype_id2name.txt
            # gene_xgene_phene_file =  gene_xgene_pheno.txt
            pm_id2consensus_seq_file = pm_id2consensus_seq.txt
            pm_id2source_pm_file = pm_id2source_pm.txt

        image_file_base = ${shared_html_base}
        gene_expression_path   = /img-static/virtualworm/Gene_Expr_Renders
        expression_object_path = /img-static/virtualworm/Expr_Object_Renders
        picture                = /img-static/pictures

        </pre_compile>

        conf_dir    = __path_to(conf)__/

        # Temporary directory in filesystem space
        # tmp_base    = __path_to(root)__/tmp/
        # tmp_base      = /tmp/wormbase/
        # In production, this is an nfs mount
        tmp_base      = /usr/local/wormbase/tmp

        #different tools WB provides
        <tool>
            <blast_blat>
                base =  /usr/local/wormbase/databases
                blast = /blast
                blat = /blat
                SCORE_KEY_IMAGE = score_key.png
                HSP_GENOME_LINK_PART_LIMIT = 10
                HSP_ALIGNMENT_IMAGE_LIMIT  = 10
                BLAST_EXEC_DIR = /usr/local/wormbase/services/blast
                BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/blat
                #BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient
            </blast_blat>
        epic
        epcr
# The 'genome' tools is used in conjunction with the 'gbrowse_base_uri' setting. More details there.
#           genome
        gmap
#       nearby_genes
            nucleotide_aligner
            protein_aligner
            tree
        rnaseq_plot
        schema
            queries
        <ontology_browser>
        association_count_file = /usr/local/wormbase/databases/%s/ontology/%s_association.%s.wb
        </ontology_browser>
            <print>
                PRO_EXEC = ./CutyCapt
            </print>
        </tool>
        <database>
            # tmp directory for sockets and lock files.
            # This *must* be distinct from above since
            # to prevent collisions of lock files in production.
            tmp = /tmp/wormbase/
            <acedb>
                # Acedb configuration
                delay = 600
                reconnect = 5
                #       host = localhost mining.wormbase.org
                host = localhost
                port = 2005
                user =
                pass =
                root = /usr/local/wormbase/acedb/wormbase
                # cache_root = __path_to(root)__/cache
                # cache_expires = 3 weeks
                # cache_size    = 100000000
                # cache_auto_purge_interval =
            </acedb>

            <mysql>
                delay = 600
                reconnect = 3
                host  = rdbms.wormbase.org
#                host  = 10.0.0.181
                user  = wormbase
                pass  = sea3l3ganz
                <data_sources>
                    clustal  = 1
                </data_sources>
            </mysql>

            <gff>
                # MySQL configuration
                delay = 600
                reconnect = 3
                # TODO: remove localhost when databases get copied over
                host = rdbms.wormbase.org
#                host = 10.0.0.181
                user = wormbase
                pass = sea3l3ganz
                <data_sources>
                    <b_malayi>
                        adaptor = DBI::mysql
                        bioproject = PRJNA10729
                    </b_malayi>
                    <c_angaria>
                        adaptor = DBI::mysql
                        bioproject = PRJNA51225
                    </c_angaria>
                    <c_brenneri>
                        adaptor = DBI::mysql
                        bioproject = PRJNA20035
                    </c_brenneri>
                    <c_briggsae>
                        adaptor = DBI::mysql
                        bioproject = PRJNA10731
                    </c_briggsae>
                    <c_elegans>
                        adaptor = DBI::mysql
                        bioproject = PRJNA13758
                    </c_elegans>
                    <c_elegans_pmap>
                        adaptor = DBI::mysql
                    </c_elegans_pmap>
                    <c_elegans_gmap>
                        adaptor = DBI::mysql
                    </c_elegans_gmap>
                    <c_inopinata>
                        adaptor = DBI::mysql
                        bioproject = PRJDB5687
                    </c_inopinata>
                    <c_japonica>
                        adaptor = DBI::mysql
                        bioproject = PRJNA12591
                    </c_japonica>
                    <c_latens>
                        adaptor = DBI::mysql
                        bioproject = PRJNA248912
                    </c_latens>
                    <c_nigoni>
                        adaptor = DBI::mysql
                        bioproject = PRJNA384657
                    </c_nigoni>
                    <c_remanei>
                        adaptor = DBI::mysql
                        bioproject = PRJNA53967
                    </c_remanei>
                    <c_tropicalis>
                        adaptor = DBI::mysql
                        bioproject = PRJNA53597
                    </c_tropicalis>
                    <o_tipulae>
                        adaptor = DBI::mysql
                        bioproject = PRJEB15512
                    </o_tipulae>
                    <o_volvulus>
                        adaptor = DBI::mysql
                        bioproject = PRJEB513
                    </o_volvulus>
                    <p_pacificus>
                        adaptor = DBI::mysql
                        bioproject = PRJNA12644
                    </p_pacificus>
                    <p_redivivus>
                        adaptor = DBI::mysql
                        bioproject = PRJNA186477
                    </p_redivivus>
                    <s_ratti>
                        adaptor = DBI::mysql
                        bioproject = PRJEB125
                    </s_ratti>
                    <t_muris>
                        adaptor = DBI::mysql
                        bioproject = PRJEB126
                    </t_muris>
                </data_sources>
            </gff>
        </database>
    </args>
</Model::WormBaseAPI>

########################################################
#
#
#   Plugins
#
#
############################################################

# Error reporting disabled automatically on
# instances with installation_type=development
<stacktrace>
    enable      1
</stacktrace>

<Plugin::ErrorCatcher>
    enable      1
    context     2
</Plugin::ErrorCatcher>

<Plugin::ErrorCatcher::Email>
    to      oicr@wormbase.org
    from    todd@wormbase.org
    use_tags 1
    subject [WB] App error on %h in %F
</Plugin::ErrorCatcher::Email>

# Session database
#<Plugin::Session>
#	expires           = 3600
#	dbi_dbh           = Schema
#	dbi_table         = sessions
#	dbi_id_field      = session_id
#	dbi_data_field    = session_data
#	dbi_expires_field = expires
#</Plugin::Session>

# Which hash elements of the data structure to return in JSON renders?
<View::JSON>
    expose_stash = data
</View::JSON>



########################################################
#
#
#   NAVBAR configuration
#
#
############################################################

<nav_bar>
    <option>
        id = about
        title = About
        url = /about\#01--10
        description = WormBase is an international consortium of biologists and computer scientists
        <nav_item>
            id = general
            title = General
            <nav_item>
                title = Mission Statement
                url = /about\#0--10
            </nav_item>
            <nav_item>
                title = Publications
            </nav_item>
            <nav_item>
                title = FAQ
                url = /about/Frequently_asked_questions
            </nav_item>
        </nav_item>
        <nav_item>
            id = people
            title = People
            <nav_item>
                title = Advisory Board
                url = /about/advisory_board
            </nav_item>
            <nav_item>
                title = WormBase Staff
                url = /about/staff\#01--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = whats_new
            title = What's New
            <nav_item>
                title = News (Blog)
                url = http://blog.wormbase.org/
            </nav_item>
            <nav_item>
                title = Release notes
                url = /about/wormbase_release_current
            </nav_item>
            <nav_item>
                title = Release Schedule
                url = /about/release_schedule
            </nav_item>
            <nav_item>
                title = Gene Name Changes
                url = /\#012-34-5
            </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = Want to know more about worm research?
                <nav_item>
                    title = Caenorhabditis Genetics Center (CGC)
                    url = http://cbs.umn.edu/cgc/home
                </nav_item>
                <nav_item>
                    title = NEMABASE
                    url = http://www.ipm.ucdavis.edu/NEMABASE/
                </nav_item>
                <nav_item>
                    title = Nematode.net
                    url = http://nematode.net/NN3_frontpage.cgi
                </nav_item>
                <nav_item>
                    title = Nematodes.org
                    url = http://www.nematodes.org/
                </nav_item>
                <nav_item>
                    title = WormAtlas
                    url = http://www.wormatlas.org/
                </nav_item>
                <nav_item>
                    title = WormBook
                    url = http://www.wormbook.org/
                </nav_item>
            </nav_item>
        </more>
    </option>
    <option>
        id = directory
        title =  Directory
        url = /search
        description = Start here to access encyclopedic information about the worm genome and its genes, proteins, and other encoded features
        <nav_item>
            id = get_started
            title = Get Started
            <nav_item>
                title = About the directory
                url = /species/all\#0123--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = search
            title = Search
            <nav_item>
                title = Basic Search
                url = /search/gene/
            </nav_item>
            <nav_item>
                title = Advanced Search
                url = /tools/queries
            </nav_item>
        </nav_item>
        <nav_item>
            id = browse
            title = Browse
            <nav_item>
                id = by_species
                title = By Species
                url = /species/all\#0123--10
                <nav_item>
                    species = c_elegans
                </nav_item>
                <nav_item>
                    species = b_malayi
                </nav_item>
                <nav_item>
                    species = c_brenneri
                </nav_item>
                <nav_item>
                    species = c_briggsae
                </nav_item>
                <nav_item>
                    species = c_japonica
                </nav_item>
                <nav_item>
                    species = c_remanei
                </nav_item>
                <nav_item>
                    species = o_volvulus
                </nav_item>
                <nav_item>
                    species = p_pacificus
                </nav_item>
                <nav_item>
                    species = s_ratti
                </nav_item>
                <nav_item>
                    species = t_muris
                </nav_item>
                <nav_item>
                    title = More…
                    url = /species/all\#0123--10
                </nav_item>
            </nav_item>
            <nav_item>
                id = by_resource
                title = By Resource
                url = /resources\#0123--10
                <nav_item>
                    title = Databases
                    url = /resources\#3--10
                </nav_item>
                <nav_item>
                    resource = gene_class
                </nav_item>
                <nav_item>
                    resource = laboratory
                </nav_item>
                <nav_item>
                    title = Methods
                    url = /resources\#2--10
                </nav_item>
                <nav_item>
                    resource = motif
                </nav_item>
                <nav_item>
                    resource = paper
                </nav_item>
                <nav_item>
                    resource = person
                </nav_item>
                <nav_item>
                    resource = wbprocess
                </nav_item>
                <nav_item>
                    resource = reagents
                </nav_item>
                <nav_item>
                    resource = transposon_family
                </nav_item>
            </nav_item>
        </nav_item>
        <nav_item>
            id = tools
            title = Tools
            <nav_item>
                title = Schema Display
                url = /tools/schema
            </nav_item>
            <nav_item>
                title = Tree Display
                url = /tools/tree
            </nav_item>
            <nav_item>
                title = Submit Data
                url = /about/userguide/submit_data#01--10
            </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = Latest updates
                <nav_item>
                    title = News (Blog)
                    url = http://blog.wormbase.org/
                </nav_item>
                <nav_item>
                    title = Release Schedule
                    url = /about/release_schedule
                </nav_item>
            </nav_item>
            <nav_item>
                title = Need help?
                <nav_item>
                    title = Nematode Nomenclature
                    url = /about/userguide/nomenclature
                </nav_item>
                <nav_item>
                    title = User's Guide
                    url = /about/userguide/for_users
                </nav_item>
                <nav_item>
                    title = FAQ
                    url = /about/Frequently_asked_questions
                </nav_item>
                <nav_item>
                    title = HelpDesk
                    url = /tools/support
                </nav_item>
            </nav_item>
        </more>
    </option>
    <option>
        id = tools
        title = Tools
        url = /tools
        description = Come explore WormBase's complex collection of information with a variety of bioinformatic tools and more
        <nav_item>
            id = get_started
            title = Get Started
            <nav_item>
                title = About our tools
                url = /about/userguide/for_users\#1--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = general_search
            title = General Search
            <nav_item>
                title = Basic Search
                url = /search/gene/
            </nav_item>
            <nav_item>
                title = Browse by Species
                url = /species/all\#0123--10
            </nav_item>
            <nav_item>
                title = Browse by Resource
                url = /resources\#0123--10
            </nav_item>
            <nav_item>
                title = Advanced Search
                url = /tools/queries
            </nav_item>
        </nav_item>
        <nav_item>
            id = by_sequence
            title = By Sequence
            <nav_item>
                title = BLAST/BLAT
                url = /tools/blast_blat
            </nav_item>
            <nav_item>
                title = e-PCR Search
                url = /tools/epcr
            </nav_item>
            <nav_item>
                title = GBrowse
                url = /tools/genome/gbrowse/
            </nav_item>
            <nav_item>
                title = Genetic Map
                url = /tools/gmap
            </nav_item>
            <nav_item>
                title = JBrowse
                url = /tools/genome/jbrowse-simple/?data=data/c_elegans_PRJNA13758
            </nav_item>
            <nav_item>
                title = Nucleotide Aligner
                url = /tools/nucleotide_aligner
            </nav_item>
            <nav_item>
                title = Protein Aligner
                url = /tools/protein_aligner
            </nav_item>
            <nav_item>
                title = Synteny Viewer
                url = /tools/synteny/mercator/
            </nav_item>
        </nav_item>
        <nav_item>
            id = by_expression
            title = By Expression
            <nav_item>
                title = SPELL
                url = https://spell.wormbase.org/
            </nav_item>
            <nav_item>
                title = Expression Dataset Locator
                url = /tools/rnaseq/expression_dataset_locator.cgi
            </nav_item>
            <nav_item>
                title = RNA-Seq FPKM Gene Search
                url = /tools/rnaseq/fpkmmine.cgi
            </nav_item>
        </nav_item>
        <nav_item>
            id = by_literature
            title = By Literature
            <nav_item>
                title = Resources: Papers
                url = /resources/paper\#1-0-2
            </nav_item>
            <nav_item>
                title = TextPresso
                url = http://www.textpresso.org/celegans/
            </nav_item>
        </nav_item>
        <nav_item>
            id = by_object
            title = By Object
            <nav_item>
                title = Schema Display
                url = /tools/schema
            </nav_item>
            <nav_item>
                title = Tree Display
                url = /tools/tree
            </nav_item>
        </nav_item>
        <nav_item>
            id = data_mining_batch_queries
            title = Data Mining and Batch Queries
            <nav_item>
                title = ParaSite BioMart
                url = http://parasite.wormbase.org/biomart/martview
            </nav_item>
            <nav_item>
                title = SimpleMine
                url = /tools/mine/simplemine.cgi
            </nav_item>
            <nav_item>
                title = Gene Set Enrichment Analysis
                url = /tools/enrichment/tea/tea.cgi
            </nav_item>
            <nav_item>
                title = WormMine
                url = http://intermine.wormbase.org/tools/wormmine/begin.do
            </nav_item>
        </nav_item>
        <nav_item>
            id = for_parasites
            title = For Parasites
            <nav_item>
                title = ParaSite
                url = http://parasite.wormbase.org
            </nav_item>
            <nav_item>
                title = ParaSite BioMart
                url = http://parasite.wormbase.org/biomart/martview
            </nav_item>
        </nav_item>
        <nav_item>
            id = for_developers
            title = For Developers
            <nav_item>
                title = Query Language
                url = /tools/queries
            </nav_item>
            <nav_item>
                title = WormBase APIs
                url = /about/userguide/for_developers\#3--10
            </nav_item>
            <nav_item>
                title = WormBase Assembly Hubs
                url = /about/userguide/wormbasehubs\#0123--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = by_ontology
            title = By Ontology
            <nav_item>
                title = Ontology Browser
                url = /tools/ontology_browser
            </nav_item>
	    <nav_item>
		title = Gene-pair Ontology Graph
		url = /tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
	    </nav_item>
	    <nav_item>
		title = Terms Ontology Graph
		url = /tools/soba/soba.cgi?action=Terms+to+SObA+Graph
	    </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = Top 3 most used tools
                <nav_item>
                    title = JBrowse
                    url = /tools/genome/jbrowse-simple/?data=data/c_elegans_PRJNA13758
                    class = tool
                </nav_item>
                <nav_item>
                    title = BLAST/BLAT
                    url = /tools/blast_blat
                    class = tool
                </nav_item>
                <nav_item>
                    title = Ontology Browser
                    url = /tools/ontology_browser
                    class = tool
                </nav_item>
            </nav_item>
            <nav_item>
                title = Need help?
                <nav_item>
                    title = User's Guide
                    url = /about/userguide/for_users
                </nav_item>
                <nav_item>
                    title = FAQ
                    url = /about/Frequently_asked_questions
                </nav_item>
                <nav_item>
                    title = HelpDesk
                    url = /tools/support
                </nav_item>
            </nav_item>
        </more>
    </option>
    <option>
        id = downloads
        title = Downloads
        url = /about/userguide\#3--10
        description = WormBase provides a large number of precomputed files to facilitate downstream analysis
        <nav_item>
            id = get started
            title = Get Started
            <nav_item>
                title = About WormBase Data
                url = /species/all\#0--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = download
            title = Download
            <nav_item>
                title = Public FTP Site
                url = ftp://ftp.wormbase.org/pub/wormbase/
            </nav_item>
            <nav_item>
                title = Listed By Species
                url = /species/all\#1--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = tools
            title = Tools
            <nav_item>
                title = Coordinates Converter
                url = /about/userguide/tools/coordinate_converter\#0--10
            </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = Commonly requested data
                <nav_item>
                    title = Latest production release
                    url = ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release
                    class = file
                </nav_item>
                <nav_item>
                    title = Latest development release
                    url = ftp://ftp.wormbase.org/pub/wormbase/releases/current-development-release
                    class = file
                </nav_item>
            </nav_item>
            <nav_item>
                title = Need help?
                <nav_item>
                    title = How to cite WormBase
                    url = /about/citing_wormbase\#0123--10
                </nav_item>
                <nav_item>
                    title = HelpDesk
                    url = /tools/support
                </nav_item>
            </nav_item>
        </more>
    </option>
    <option>
        id = community
        title = Community
        url = /about/userguide\#2--10
        description = Come join and connect with worm experts online and beyond
        <nav_item>
            id = directories
            title = Directories
            <nav_item>
                title = Find a Colleague
                url = /resources/person\#1-0-2
            </nav_item>
            <nav_item>
                title = Worm Labs
                url = /resources/laboratory\#012--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = get_involved
            title = Get Involved
            <nav_item>
                title = Meetings
                url = /\#012-43-5
            </nav_item>
            <nav_item>
                title = Worm Community Forum
                url = http://forums.wormbase.org
            </nav_item>
            <nav_item>
                title = WormBase Wiki
                url = http://wiki.wormbase.org
            </nav_item>
            <nav_item>
                title = Submit Data
                url = /about/userguide/submit_data#01--10
            </nav_item>
        </nav_item>
        <nav_item>
            id = resources
            title = Resources
            <nav_item>
                title = Key Papers
                url = /species/c_elegans\#1--10
            </nav_item>
            <nav_item>
                title = Caenorhabditis Genetics Center (CGC)
                url = http://cbs.umn.edu/cgc/home
            </nav_item>
            <nav_item>
                title = NEMABASE
                url = http://www.ipm.ucdavis.edu/NEMABASE/
            </nav_item>
            <nav_item>
                title = Nematode.net
                url = http://nematode.net/NN3_frontpage.cgi
            </nav_item>
            <nav_item>
                title = Nematodes.org
                url = http://www.nematodes.org/
            </nav_item>
            <nav_item>
                title = WormAtlas
                url = http://www.wormatlas.org/
            </nav_item>
            <nav_item>
                title = WormBook
                url = http://www.wormbook.org/
            </nav_item>
            <nav_item>
                title = For Developers
                url = /about/userguide/for_developers\#012345--10
            </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = External links
                <nav_item>
                    title = WormBase Blog
                    url = http://blog.wormbase.org/
                </nav_item>
                <nav_item>
                    title = WormBase@Twitter
                    url = http://www.twitter.com/wormbase
                    class = twitter
                </nav_item>
                <nav_item>
                    title = WormBase@GitHub
                    url = http://github.com/wormbase
                    class = github
                </nav_item>
            </nav_item>
        </more>
    </option>
    <option>
        id = support
        title = Support
        url = /about/userguide\#0123456--10
        description = We've created different user guides for distinct interests and experience levels
        <nav_item>
            id = general
            title = General
            <nav_item>
                title = Nematode Nomenclature
                url = /about/userguide/nomenclature
            </nav_item>
            <nav_item>
                title = User's Guide
                url = /about/userguide/for_users
            </nav_item>
            <nav_item>
                title = WormBaseHD YouTube
                url = https://www.youtube.com/user/WormBaseHD
            </nav_item>
            <nav_item>
                title = Submit Data
                url = /about/userguide\#15--10
            </nav_item>
            <nav_item>
                title = FAQ
                url = /about/Frequently_asked_questions
            </nav_item>
        </nav_item>
        <nav_item>
            id = for_developers
            title = For developers
            <nav_item>
                title = Developer's Guide
                url = /about/userguide/for_developers\#012345--10
            </nav_item>
            <nav_item>
                title = REST API Documentation
                url = /about/userguide/for_developers/api-rest
            </nav_item>
            <nav_item>
                title = Data Models
                url = http://wiki.wormbase.org/index.php/WormBase_Models
            </nav_item>
            <nav_item>
                title = Staff Documentation
                url = /about/internal_documentation\#012--10
            </nav_item>
            <nav_item>
                title = Query Search Language
                url = /tools/queries
            </nav_item>
        </nav_item>
        <more>
            <nav_item>
                title = Still have questions?
                <nav_item>
                    title = Contact HelpDesk
                    url = /tools/support
                </nav_item>
            </nav_item>
        </more>
    </option>
</nav_bar>


# Search box dropdown
#    A quick list of available searches.
#    Remove entries from here to
#    prevent them from appearing as an option in the navbar
#    global search drop down menu.
#    Order is important.

<search_dropdown>
#     <option>
#         title = Analysis
#         id    = analysis
#     </option>
    <option>
        title = All
        id    = all
    </option>
    <option>
        title = Anatomy
        id    = anatomy_term
    </option>
    <option>
        title = Antibody
        id    = antibody
    </option>
    <option>
        title = Clone
        id    = clone
    </option>
    <option>
        title = Expression pattern
        id    = expr_pattern
    </option>
    <option>
        title = Gene
        id    = gene
    </option>
    <option>
         title = Gene Class
         id    = gene_class
    </option>
    <option>
        title = Gene Ontology
        id    = go_term
    </option>
    <option>
        title = Human Disease
        id    = disease
    </option>
#    <option>
#        title = Issues
#        id    = issue
#    </option>
    <option>
        title = Laboratory
        id    = laboratory
    </option>
    <option>
         title = Life Stage
         id    = life_stage
    </option>
    <option>
         title = Molecule
         id = molecule
    </option>
    <option>
        title = Paper
        id    = paper
    </option>
    <option>
        title = Person
        id    = person
    </option>
    <option>
        title = Phenotype
        id    = phenotype
    </option>
    <option>
        title = Protein
        id    = protein
    </option>
    <option>
        title = Rearrangement
        id    = rearrangement
    </option>
#     <option>
#         title = Sequence
#         id    = sequence
#     </option>
    <option>
        title = Sequence Feature
        id    = feature
    </option>
    <option>
        title = Strain
        id    = strain
    </option>
    <option>
        title = Transgene
        id    = transgene
    </option>
    <option>
        title = Variation
        id    = variation
    </option>
</search_dropdown>





########################################################
#
#
# Website sections: species, tools, resources, me.
#
#  This section configures the available pages, widgets
#  and fields for each section of the application.
#
#  REMEMBER: If you change the name of anything here,
#  you will also need to change the name of the
#  corresponding method in the Model class and the name
#  of the template
#
############################################################


<sections>

  ######################################
  #
  # Species pages.
  #
  #   (Pages available on a per-species
  #    basis are configured in the
  #    <species_list> stanza.)
  #
  ######################################
  <species>
    title = Species

    # General structure
    # <class_name> -- A symbolic name for the class
    #     title    -- Formal title of the class
    #     <browse>
    #         limits =
    #         limits =
    #     </browse>
    #     <search> -- methods to call hen displaying search results
    #         fields = example
    #         fields = example2
    #     </search>
    #     <widgets>
    #         <widget1>                          -- one or more widgets
    #             name     = example             -- symbolic name for the widget
    #             title    = My Example          -- display name for the widget
    #             display  = [report|index|both] -- where to display the widget (use index for class index, report for summary page)
    #             tooltip  = my tooltip          -- brief tooltip, eg: This is a tooltip.
    #             precache = [0|1]               -- boolean whether to precache the page
    #             fields   = examplefield        -- one or more fields that correspond to model methods and template name.
    #         </widget1>
    #     </widgets>
    #     <tools>     -- list of tools available for this class.
    #     </tools>
    # </class_name>

    <anatomy_term>
    title = Anatomy term
    precache = true
    <browse>
        limits = Species
        limits = Anatomy_term
    </browse>
    <search>
        fields name
        fields definition
    </search>
    <default_widgets>
        overview
        associations
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            tooltip A concise overview of this Anatomy Term
            display report
            fields name
            fields term
            fields definition
            fields synonyms
            fields transgenes
            fields expression_patterns
            fields gene_ontology
            fields anatomy_functions
            fields anatomy_function_nots
            fields expression_clusters
            fields wormatlas
        </overview>
        <associations>
            name associations
            title Associations
            tooltip Associations to this Anatomy Term
            display report
            fields transgenes
            fields expression_patterns
            fields gene_ontology
            fields anatomy_functions
            fields anatomy_function_nots
            fields expression_clusters
        </associations>
        <expression_markers>
            name expression_markers
            title Expression markers
            tooltip Expression markers
            display report
            field markers
        </expression_markers>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to third party resources.
            fields  xrefs
        </external_links>
        <ontology_browser>
            name ontology_browser
            title Ontology Browser
            tooltip Anatomy Term Browser
            display report
            fields name
        </ontology_browser>
        <references>
            name  references
            title References
            display report
            tooltip Publications that describe the creation or use of this anatomy term.
            fields references
        </references>
    </widgets>
        <tools>
        </tools>
    </anatomy_term>

    <antibody>
    title = Antibody
    precache = true
    <browse>
        limits = Species
        limits = Gene_class
    </browse>
    <search>
        fields = name
        fields = corresponding_gene
        fields = summary
    </search>
    <default_widgets>
        overview
        expression
    </default_widgets>
    <widgets>
        <overview>
            name   overview
            title  Overview
            display report
            tooltip A concise overview of the construction and localization of this antibody.
            fields name
            fields other_names
            fields summary
            fields corresponding_gene
            fields antigen
            fields animal
            fields clonality
            fields laboratory
            fields constructed_by
            fields remarks
            fields historical_gene
        </overview>
        <expression>
            name   expression
            title  Expression
            display report
            tooltip Expression patterns generated using the antibody.
            fields expression_patterns
        </expression>
        <references>
            name  references
            title References
            display report
            tooltip Publications that describe the creation or use of this antibody.
            fields references
        </references>
        </widgets>
        <tools>
        </tools>
    </antibody>

   <cds>
      title = CDS
      precache = true
      <browse>
          limits = Species
          limits = Gene_class
      </browse>
      <search>
          fields = name
          fields = taxonomy
          fields = description
      </search>
      <default_widgets>
          overview
          sequences
      </default_widgets>
      <widgets>
        <overview>
            name overview
            title Overview
            display report
            tooltip An overview of the CDS object.
            fields name
            fields taxonomy
            fields description
            fields sequence_type
            fields identity
            fields remarks
            fields corresponding_all
            fields partial
            fields method
        </overview>
        <expression>
            name expression
            title Expression
            display report
            tooltip Expression patterns and data, including images from publications and time-lapse movies.
         #   fields fpkm_expression_summary_ls # now load with ajax
        </expression>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to third party resources.
            fields  xrefs
        </external_links>
        <location>
            name location
            title Location
            display report
            tooltip The genomic location of the CDS.
            fields genomic_position
            fields genomic_image
            fields tracks
            fields genetic_position
        </location>
        <reagents>
            name reagents
            title Reagents
            display report
            tooltip Reagents related to the CDS.
            fields microarray_assays
            fields orfeome_assays
            fields source_clone
            fields pcr_products
            fields matching_cdnas
        </reagents>
        <sequences>
            name sequences
            title Sequences
            display report
            tooltip Sequences and homologies.
            fields print_blast
            fields print_sequence
          # fields print_homologies
            fields predicted_exon_structure
            fields predicted_units
          #  fields transcripts
        </sequences>
        <feature>
            name feature
            title Sequence features
            display report
            tooltip Sequence features associated with this CDS
            fields features
        </feature>
      </widgets>
      <tools>
          nucleotide_aligner
      </tools>
    </cds>

    <clone>
    title = Clone
    precache = true
    <browse>
        limits = Species
        limits = Gene_class
    </browse>
    <search>
        fields = name
        fields = type
        fields = remarks
    </search>
    <default_widgets>
        overview
        location
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            display report
            tooltip An overview of the clone.
            fields name
            fields type
            fields sequences
            fields lengths
            fields maps
            fields sequence_status
            fields canonical_for
            fields canonical_parent
            fields screened_positive
            fields screened_negative
            fields gridded_on
            fields remarks
            fields taxonomy
            fields url
            fields in_strain
            fields pcr_product
            fields expression_patterns
            fields genomic_position
        </overview>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to third party resources.
            fields  xrefs
        </external_links>
        <location>
            name location
            title Location
            display report
            tooltip Genomic location of this clone.
            fields genomic_position
            fields genomic_image
            fields tracks
            fields jbrowse_tracks
        </location>
        <sequences>
            name sequences
            title Sequences
            display report
            tooltip Sequences and homologies.
            fields print_sequence
            fields predicted_units
            fields strand
            fields sequences
            fields end_reads
        </sequences>
        <references>
            name references
            title References
            display report
            tooltip References that cite this clone.
        </references>
    </widgets>
    <tools>
    </tools>
    </clone>

    <construct>
        title = Construct
        precache = true
        <browse>
            limits = Species
        </browse>
        <search>
            fields = name
            fields = summary
            fields = remarks
        </search>
        <default_widgets>
            overview
            isolation
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of this construct.
                display report
                fields name
                fields summary
                fields driven_by_gene
                fields gene_product
                fields type_of_construct
                fields fusion_reporter
                fields other_reporter
                fields utr
                fields selection_marker
                fields construction_summary
                fields remarks
                fields used_for
            </overview>
            <isolation>
                name isolation
                title Construction details
                tooltip construction details of this construct.
        #		fields person
                fields construction_summary
                fields laboratory
                fields clone
                fields historical_gene
        #		fields recombination_site
            </isolation>
            <expr_pattern>
                name   expr_pattern
                title  Expression
                tooltip Expression details of this transgene.
                display report
                fields expression_patterns
        #		fields marker_for
        #		fields marked_rearrangement
            </expression>
            <references>
                name references
                title References
                display report
                tooltip Publications citing this construct.
            </references>
            <transgene>
                name transgene
                title Transgene
                tooltip Transgenes generated by this construct.
                display report
                fields transgenes
            </transgene>
    #		# The shared phenotypes* methods and phenotypes.tt2 widget.
    #		<gene_regulation>
    #			name gene_regulation
    #			title Gene Regulation
    #			tooltip Gene regulation of the construct.
    #			display report
    #			fields phenotypes
    #		</gene_regulation>
        </widgets>
        <tools>
        </tools>
    </construct>

    <expression_cluster>
    title = Expression cluster
    precache = true
        <browse>
        limits = Species
        limits = Gene_class
        </browse>
        <search>
        fields = name
        fields = algorithm
        fields = description
        fields = remarks
        </search>
        <default_widgets>
          overview
          regulation
          associations
          references
        </default_widgets>
        <widgets>
        <overview>
            name overview
            title  Overview
            display report
            tooltip A concise overview of the expression cluster.
            fields name
            fields description
            fields remarks
            fields algorithm
      fields taxonomy
      fields attribute_of
        </overview>
        <genes>
            name   genes
                    title  Genes
                    display report
                    tooltip Genes contained in the expression cluster.
                fields genes
                </genes>
        <associations>
            name   associations
                    title  Associations
                    display report
                    tooltip Associated annotations of genes in the expression cluster.
                    fields anatomy_terms
                  fields life_stages
                  fields go_terms
                  fields processes
                </associations>
                <clustered_data>
            name clustered_data
                    title  Clustered data
                    display report
                    tooltip Clustered data related to this expression cluster.
                    fields microarray
                    fields sage_tags
                </clustered_data>
              <regulation>
                name regulation
                title Regulation
                display report
                fields regulated_by_gene
                fields regulated_by_treatment
                fields regulated_by_molecule
              </regulation>
                <references>
            name   references
                    title  References
                    display report
                    tooltip References that cite this expression cluster.
                </references>
        </widgets>
        <tools>
        </tools>
    </expression_cluster>

    <expr_pattern>
    title = Expression pattern
        precache = true
    <browse>
        limits = Species
        limits = Gene_class
    </browse>
    <search>
        fields = name
        fields = description
    </search>
        <advanced_search>
        <element>
                name = name
            type = textbox
        </element>
        <element>
            name = anatomy_term
            type = textbox
        </element>
        <element>
            name = life_stage
            type = textbox
        </element>
        </advanced_search>
    <default_widgets>
                 overview
         details
         references
    </default_widgets>
    <widgets>
        <overview>
            name   overview
            title  Overview
                    display report
                    tooltip An overview of the expression pattern.
                    fields name
                    fields expression_image
                    fields description
                    fields is_bc_strain
                    fields subcellular_locations
                    fields remarks
                  fields curated_images
                  fields historical_gene
                  fields ep_movies
                  fields database
                </overview>
                <details>
            name details
                    title Details
                    display report
                    tooltip Experimental details of the expression pattern.
                    fields name
                    fields expressed_by
                    fields expressed_in
                    fields anatomy_ontology
                    fields sequence_feature
            fields gene_ontology
                    fields experimental_details
                </details>
                <references>
            name references
                    title References
                    display report
                    tooltip Publications citing this expression pattern.
                </references>
          </widgets>
          <tools>
          </tools>
    </expr_pattern>

    <expr_profile>
    title = Expression profile
    precache = true
    <browse>
    </browse>
    <search>
    </search>
    <default_widgets>
        overview
        </default_widgets>
        <widgets>
        <overview>
            name overview
            title Overview
            tooltip A concise overview for this Expr_profile
            display report
            fields name
            fields remarks
            fields method
                    fields pcr_data
                fields profiles
                fields pcr_products
                fields expression_map
                fields rnai
            </overview>
        </widgets>
        <tools>
        </tools>
    </expr_profile>

    <feature>
        title = Sequence feature
        precache = true
        <browse>
            limits = Species
            limits = Feature
        </browse>
        <search>
            fields = name
            fields = description
            fields = taxonomy
        </search>
        <default_widgets>
            overview
            associations
            molecular_details
            location
            evidence
        </default_widgets>
        <widgets>
          <overview>
             name   overview
             title  Overview
             display report
             tooltip A brief overview of the current feature.
             fields name
             fields other_names
             fields taxonomy
             fields defined_by
             fields method
             fields description
             fields remarks
             fields sequence_ontology_terms
             fields binds_gene_product
             fields transcription_factor
             fields associated_gene
          </overview>
          <associations>
             name   associations
             title  Associations
             display report
             tooltip Feature associations.
             fields associations
             fields binds_gene_product
             fields transcription_factor
          </associations>
          <location>
               name location
               title Location
               display report
               tooltip The genomic location of the CDS.
               fields genomic_position
               fields genomic_image
               fields tracks
               fields genetic_position
          </location>
          <molecular_details>
               name molecular_details
               title Molecular Details
               tooltip Molecular details about the sequence feature.
               display report
               fields flanking_sequences
               fields dna_text
          </molecular_details>
          <history>
              name history
              title History
              display report
              tooltip WormBase curatorial history for the sequence feature.
              fields history_lite
          </history>
          <evidence>
              name evidence
              title Evidence
              display report
              tooltip Evidence
              fields defined_by
              fields remarks
          </evidence>
        </widgets>
        <tools>
        </tools>
    </feature>

#    # The Feature_data Summary
#    # TH: 2011.05.29: Complete
#    # This isn't currently a page and probably never should be.
#    # * needs search and browse params
#    <feature_data>
#	title = Feature data
#        <browse>
#        </browse>
#        <search>
#        </search>
#        <widgets>
#		<overview>
#			name overview
#                   title Overview
#                   tooltip A concise overview for this object.
#                   display report
#                   fields name
#                   fields method
#                   fields feature
#                   fields intron
#                   fields predicted_five_prime
#                   fields predicted_three_prime
#		</overview>
#        </widgets>
#        <tools>
#        </tools>
#    </feature_data>

    <gene>
        title = Gene
        precache = true
        <browse>
        limits  = Species
            limits  = Gene_class
            display = index
        </browse>
        <search>
        fields = name
            fields = taxonomy
            fields = concise_description
        </search>
        <layout>
          default = 0-9f-10
          citation = d-j-10
        </layout>
        <default_widgets>
            overview
            location
        sequences
        </default_widgets>
        <widgets>
        <overview>
        name overview
        title Overview
        display report
        tooltip Provides a concise description of gene function (if available) and most commonly used names.
        fields also_refers_to
                fields classification
                fields cloned_by
                fields concise_description
                fields legacy_information
                fields locus_name
                fields name
                fields gene_class
                fields gene_cluster
                fields other_names
                fields sequence_name
                fields status
                fields merged_into
                fields structured_description
                fields taxonomy
                fields version
                fields human_disease_relevance
                fields operon
                fields clone
                fields named_by
                fields remarks
                fields transposon
                fields parent_sequence
            </overview>
            <expression>
                name expression
                title Expression
                display report
                tooltip Expression patterns and data, including images from publications and time-lapse movies.
                fields anatomic_expression_patterns
                fields expression_profiling_graphs
            #    fields expression_patterns # replaced by d-to-c specific fields expressed_in, expressed_during, subcellular_localization
                fields anatomy_terms
                fields expression_cluster
                fields fourd_expression_movies
                fields microarray_topology_map_position
                fields anatomy_function
            #    fields fpkm_expression_summary_ls  # now load with ajax
            </expression>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <genetics>
                name genetics
                title Genetics
                display report
                tooltip Genetic information such as alleles and rearrangements that affect the gene.
                fields alleles
                fields alleles_count   # count for alleles other and polymorphisms
           #     fields alleles_other  # as async loaded field
           #     fields polymorphisms  # as async loaded field
                fields rearrangements
                fields reference_allele
                fields strains
            </genetics>
            <gene_ontology>
        name gene_ontology
                title Gene Ontology
                display report
                tooltip Curated and computationally assigned gene ontology associations.
                fields gene_ontology
                fields gene_ontology_summary
            </gene_ontology>
            <history>
        name history
                title History
                display report
                tooltip WormBase curatorial history for the gene.
                fields history
                fields old_annot
            </history>
            <homology>
        name   homology
                title  Homology
                display report
                tooltip Precalculated similaries for the gene, including homologs and orthologs
                fields best_blastp_matches
                fields nematode_orthologs
                fields other_orthologs
                fields paralogs
                fields protein_domains    # Not sure this belongs here.
                fields treefam
            </homology>
            <interactions>
        name interactions
                title Interactions
                display report
                tooltip Genetic, protein, and predicted interactions.
                fields interactions
            </interactions>
            <mapping_data>
              name mapping_data
              title Mapping data
              tooltip Mapping data for the gene
              display report
              fields two_pt_data
              fields multi_pt_data
              fields pos_neg_data
            </mapping_data>
            <location>
        name location
                title Location
                display report
                tooltip Display the genetic and physical coordinates of the gene (if known).
                fields genomic_position
                fields genomic_image
                fields genetic_position
                fields tracks
            </location>
            <phenotype>
        name phenotypes
                title Phenotypes
                display report
                tooltip Phenotypes associated with this gene.
                fields phenotype
                fields phenotype_not_observed
                fields phenotype_by_interaction
        fields drives_overexpression
            </phenotype>
            <reagents>
        name reagents
                title Reagent
                display report
                tooltip Experimental reagents.
                fields antibodies
                fields matching_cdnas
                fields microarray_probes
                fields orfeome_primers
                fields primer_pairs
                fields sage_tags
                fields transgenes
                fields transgene_products
            </reagents>
            <references>
        name references
                title References
                display report
                tooltip Publications citing this gene.
            </references>
            <sequences>
        name sequences
                title Sequences
                display report
                tooltip Sequences corresponding to the gene, including gene models, CDSs, transcripts, and conceptual translations
                fields gene_models
            </sequences>
            <feature>
                name feature
                title Sequence features
                display report
                tooltip Sequence features associated with this gene
		fields feature_image
                fields features
            </feature>
            <human_diseases>
                name human_diseases
                title Human Diseases
                display report
                tooltip human diseases related to this gene
                fields human_disease_relevance
                fields human_diseases
            </human_diseases>
        </widgets>
        <tools>
            gmap
#           nearby_genes
            nucleotide_aligner
        </tools>
    </gene>

    <gene_cluster>
        title = Gene cluster
    precache = true
        <browse>
        limits  = Species
        display = index
        </browse>
        <search>
        fields = name
                fields = taxonomy
        </search>
        <default_widgets>
        overview
        </default_widgets>
        <widgets>
        <overview>
            name overview
                    title Overview
                    tooltip A concise overview for this Gene_cluster.
                    display report
                    fields name
                    fields description
                    fields title
                    fields contains_genes
                </overview>
        </widgets>
        <tools>
        </tools>
    </gene_cluster>

    # The GO_term Summary
    <go_term>
        title = GO term
        precache = true
        <browse>
        </browse>
        <search>
          fields name
          fields definition
        </search>
        <default_widgets>
            overview
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of this Gene Ontology Term
                display report
                fields name
                fields term
                fields definition
                fields type
            </overview>
            <associations>
                name associations
                title Associations
                tooltip Annotations for this term
                display report
                fields genes
                fields genes_summary
                fields cds
                fields motif
                fields sequence
                fields transcript
                fields anatomy_term
                fields homology_group
                fields phenotype
                #fields expr_pattern
                fields cell
            </associations>
            <ontology_browser>
                name ontology_browser
                title Ontology Browser
                display report
                tooltip This would be the tooltip.
                fields name
            </ontology_browser>
        </widgets>
        <tools>
        </tools>
    </go_term>

    <homology_group>
        title = Homology group
        precache = true
        <browse>
        </browse>
        <search>
        </search>
        <default_widgets>
        overview
        </default_widgets>
        <widgets>
        <overview>
            name overview
                    title Overview
                    tooltip A concise overview for this Homology_group
                    display report
                    fields name
                    fields remarks
                fields title
                fields type
                fields gene_ontology_terms
                fields proteins
            </overview>
                <external_links>
            name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
                </external_links>
        </widgets>
        <tools>
        </tools>
    </homology_group>

    <interaction>
        title = Interaction
        precache = true
        <browse>
        limits = Species
        limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = remarks
        </search>
        <default_widgets>
        overview
        </default_widgets>
        <widgets>
        <overview>
            name    overview
            title   Overview
            display report
            tooltip An overview of the interaction object.
            fields name
            fields remarks
            fields laboratory
            fields interaction_type
            fields interaction_subtype
            fields interaction_summary
            fields regulation_level
            fields regulation_result
            fields detection_method
            fields libraries_screened
            fields confidence
            fields interaction_phenotype
            fields rnai
            fields process
            fields interactor
            fields historical_gene
        </overview>
        <interactions>
            name    interactions
            title   Interactors
            display report
            tooltip Interactor details.
            fields interactions
      fields interaction_type
        </interactions>
                <external_links>
            name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
                </external_links>
        <references>
            name references
            title References
            tooltip References that refer to this lifestage.
            display reports
            fields references
        </references>
         </widgets>
    </interaction>

    <life_stage>
        title = Life stage
        precache = true
        <browse>
            limits = Species
            limits = Life_stage
        </browse>
        <search>
            fields name
            fields definition
            fields remarks
        </search>
        <default_widgets>
            overview
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip A concise overview of this life stage.
                fields name
                fields definition
                fields contained_in_life_stage
                fields preceded_by_life_stage
                fields followed_by_life_stage
                fields substages
                fields other_names
                fields cells
                fields cell_group
                fields remarks
            </overview>
            <expression>
                name   expression
                title  Expression
                display report
                tooltip Expression patterns that span this life stage.
                fields expression_patterns
            </expression>
# Removed at request of Wen Chen, 2011.02.14. Cell/Cell_group
# and Anatomy_term aren't linked to the Lifestage class anymore
# even though they are still present.
#           <anatomy>
#                 name anatomy
#                 title Anatomy
#                 tooltip This would be the tooltip.
#                 fields cells
#        fields cell_group
#               </anatomy>
            <references>
                name references
                title References
                tooltip References that refer to this lifestage.
                display reports
                fields references
            </references>
            <ontology_browser>
                name ontology_browser
                title Ontology Browser
                tooltip Life Stage Term Browser
                display report
                fields name
            </ontology_browser>
        </widgets>
        <tools>
        </tools>
    </life_stage>

    <microarray_results>
        title = Microarray results
        <browse>
            limits = Species
            limits = Motif
        </browse>
        <search>
            fields = name
            fields = gene
            fields = cds
        </search>
        <default_widgets>
            overview
            experiments
        </default_widgets>
            <widgets>
            <overview>
                name overview
                        title Overview
                        tooltip A concise overview for this microarray result.
                        display report
                precache true
                        fields gene
                        fields cds
                fields transcript
                fields pseudogene
                fields name
                </overview>
            <experiments>
                name experiments
                        title Experiments
                        tooltip Details about the experiments associated with this microarray result.
                        display report
                precache true
                fields range
                fields results
                fields microarray
                </experiments>
            </widgets>
        <tools>
        </tools>
    </microarray_results>



    <operon>
        title = Operon
        precache = true
        <browse>
        </browse>
        <search>
        </search>
        <default_widgets>
            overview
            location
            structure
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview for this Operon
                display report
                fields name
                fields description
                fields species
                fields remarks
            </overview>
            <location>
                name location
                title Location
                display report
                tooltip The genomic location of the operon.
                fields genomic_position
                fields genomic_image
                fields tracks
                fields genetic_position
            </location>
            <structure>
                name structure
                title Structure
                tooltip A details on the structure of the operon.
                display report
                fields structure
            </structure>
        </widgets>
        <tools>
        </tools>
    </operon>

    # The Position_matrix Summary
    # TH: 2011.05.30: Complete
    # * has hard-coded path to the position_matrix directory
    # * how are flat files created?
    # * associated* methods return scalars. Correct? If not, pluralize method names, fix methods and templates.
    # * data structure in postion_data needs to be dissected and formated in tt2
    # * no support for images
    <position_matrix>
        title = Position matrix
        precache = true
        <browse>
        </browse>
            <search>
            </search>
            <default_widgets>
            overview
            </default_widgets>
            <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview for this Position_matrix
                display report
                            fields name
                fields description
                fields remarks
                fields associated_feature
                fields associated_position_matrix
                fields consensus
                fields position_data
                fields bound_by_gene_product
                fields transcription_factor
            </overview>
        </widgets>
        <tools>
        </tools>
    </position_matrix>

    # The combined PCR_product/Oligo summary report
    <pcr_oligo>
    title = PCR Product/Oligo
    precache = true
    <default_widgets>
        overview
        sequence
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            tooltip A concise overview of this PCR/Oligo set.
            display report
            fields name
            fields canonical_parent
            fields oligos
            fields overlapping_genes
            fields overlaps_CDS
            fields overlaps_transcript
            fields overlaps_pseudogene
            fields overlaps_variation
            fields on_orfeome_project
            fields remarks
            fields microarray_results
            fields segment
            fields amplified
            fields laboratory
            fields SNP_loci
            fields assay_conditions
            fields in_sequences
            fields pcr_products
            fields rnai
            fields source
            fields assay_conditions
        </overview>
        <location>
            name location
            title Location
            display report
            tooltip The genomic location of the PCR/Oligo.
            fields genomic_position
            fields genomic_image
            fields tracks
            fields jbrowse_tracks
            fields genetic_position
        </location>
        <sequence>
            name sequence
            title Sequence
            tooltip Sequence of the PCR product / oligo set.
            display report
            fields name
            fields segment
            fields oligos
        </sequence>
    </widgets>
    <tools>
    </tools>
    </pcr_oligo>

    <phenotype>
        title = Phenotype
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = description
        </search>
        <default_widgets>
            overview
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip A brief overview of this phenotype.
                fields name
                fields synonyms
                fields related_phenotypes
                fields description
                fields is_dead
                fields remarks
            </overview>
            <ontology_browser>
                name ontology_browser
                title Ontology Browser
                display report
                tooltip This would be the tooltip.
                fields name
            </ontology_browser>
            <rnai>
                name rnai
                title RNAi
                display report
                tooltip This would be the tooltip.
                fields rnai
                fields rnai_not
            </rnai>
            <variation>
                name    variation
                title   Variation
                tooltip This would be the tooltip.
                display report
                fields  variation
                fields  variation_not
            </variation>
            <go_term>
                name   go_term
                title  Gene Ontology
                display report
                tooltip This would be the tooltip.
                fields go_term
            </go_term>
            <transgene>
                name   transgene
                title  Transgene
                display report
                tooltip This would be the tooltip.
                fields transgene
                fields transgene_not
            </transgene>
            <associated_anatomy>
                name   associated_anatomy
                title  Associated Anatomy
                display report
                tooltip This would be the tooltip.
                fields associated_anatomy
            </associated_anatomy>
        </widgets>
        <tools>
        </tools>
    </phenotype>

    <protein>
        title = Protein
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = taxonomy
            fields = description
            fields = corresponding_gene
        </search>
        <default_widgets>
            overview
            sequences
        </default_widgets>
        <widgets>
            <overview>
                name   overview
                title  Overview
                display report
                tooltip A concise overview of this protein.
                fields name
                fields taxonomy
                fields description
                fields type    # this is the curation status of ONE CDS. Relevant?
                fields status
                fields remarks
                fields estimated_molecular_weight
                fields estimated_isoelectric_point
                fields best_human_match
                fields pfam_graph
                fields corresponding_all
            </overview>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <history>
                name history
                title History
                display report
                tooltip Curatorial history of this protein.
                fields history
            </history>
            <homology>
                name   homology
                title  Homology
                display report
                tooltip Protein homology and orthology; protein domain motifs.
                fields homology_groups
                # fields orthologs  # comment out due to Ortholog_gene is no longer available
                fields best_blastp_matches
                fields homology_image
                fields pfam_graph
                fields homology_image # so field won't be disabled
            </homology>
            <location>
                name location
                title Location
                display report
                tooltip Display the genetic and physical coordinates of the protein coding gene.
                fields genomic_position
                fields genomic_image
                fields genetic_position
                fields tracks
            </location>
            <sequences>
                name   sequences
                title  Sequences
                display report
                tooltip Molecular details of the protein, including its sequence.
                fields sequence
                fields estimated_molecular_weight
                fields estimated_isoelectric_point
                fields amino_acid_composition
            </sequences>
            <motif_details>
                name motif_details
                title Motif Details
                display report
                fields motif_details
            </motif_details>
        </widgets>
        <tools>
            protein_aligner
        </tools>
    </protein>

    <rearrangement>
        title = Rearrangement
        precache = true
        <default_widgets>
            overview
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of the rearrangement.
                display report
                fields name
                fields type
                fields chromosome
                fields positive
                fields negative
                fields display
                fields strains
                fields reference_strain
                fields mapping_data
                fields remarks
            </overview>
            <isolation>
                name isolation
                title Isolation
                display report
                tooltip Isolation information for this Rearrangement.
                fields author
                fields source
                fields derived
                fields laboratory
                fields mutagen
                fields date
            </isolation>
            <phenotypes>
                name phenotypes
                title Phenotypes
                display report
                tooltip Phenotypes observed and not observed in this Rearrangement.
                fields phenotypes
                fields phenotypes_not_observed
            </phenotypes>
            <references>
                name references
                title References
                display report
                tooltip Publications citing this Rearrangement.
                precache true
            </references>
        </widgets>
        <tools>
            gmap
        </tools>
    </rearrangement>

    <rnai>
        title = RNAi
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = taxonomy
        </search>
        <default_widgets>
            overview
            details
            phenotypes
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip A brief overview of this RNAi experiment.
                fields name
                fields historical_name
                fields laboratory
                fields taxonomy
                fields remarks
                fields targets
                    # fields interactions  # not yet supported
            </overview>
            <details>
                name    details
                title   Details
                display report
                tooltip Details of the RNAi experiment.
                fields reagent
                fields sequence
                fields assay
                fields genotype
                fields strain
                fields treatment
                fields life_stage
                fields delivered_by
            </details>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <movies>
                name    movies
                title   Movies
                display report
                tooltip Movies demonstrating phenotypes from the RNAi experiment.
                fields  movies
            </movies>
            <phenotypes>
                name phenotypes
                title Phenotypes
                display report
                tooltip Phenotypes observed and not observed in this RNAi experiment.
                fields phenotypes
                fields phenotypes_not_observed
            </phenotypes>
            <references>
                name references
                title References
                tooltip References that cite this RNAi experiment.
                display report
                fields xrefs
            </references>
        </widgets>
        <tools>
        </tools>
    </rnai>

    <sequence>
        title = Sequence
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = taxonomy
            fields = description
        </search>
        <default_widgets>
            overview
            sequences
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip An overview of the sequence object.
                fields name
                fields taxonomy
                fields description
                fields sequence_type
                fields identity
                fields method
                fields remarks
                fields laboratory
                fields available_from
                fields analysis
                fields source_clone
                fields subsequence
                fields paired_read
                fields cdss
                fields transcripts
                fields pseudogenes
            </overview>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <location>
                name location
                title Location
                display report
                tooltip The genomic location of the sequence.
                fields genomic_position
                fields genomic_image
                fields tracks
                fields genetic_position
            </location>
            <reagents>
                name reagents
                title Reagents
                display report
                tooltip Reagents related to the sequence.
                fields microarray_assays
                fields orfeome_assays
                fields source_clone
                fields matching_cdnas
                fields pcr_products
                fields library
            </reagents>
            <sequences>
                name sequences
                title Sequences
                display report
                tooltip Sequences and homologies.
                fields print_sequence
    #           fields print_homologies
                fields transcripts
                fields predicted_units
    #             fields print_feature
                fields strand
            </sequences>
        </widgets>
        <tools>
            nucleotide_aligner
        </tools>
    </sequence>

    <strain>
        title = Strain
        precache = true
        <browse>
            limits = Species
        </browse>
        <search>
            fields = name
            fields = genotype
            fields = taxonomy
        </search>
        <default_widgets>
            overview
            origin
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip A concise overview of the strain.
                fields name
                fields taxonomy
                fields genotype
                fields mutagen
                fields outcrossed

                fields remarks
                fields other_names
            </overview>
            <contains>
                name contains
                title Contains
                display report
                fields genes
                fields alleles
                fields rearrangements
                fields clones
                fields transgenes
            </contains>
            <human_diseases>
                name human_diseases
                title Human diseases
                display report
                fields detailed_disease_model
            </human_diseases>
            <natural_isolates>
                name natural_isolates
                title Natural Isolates
                tooltip This widget displays information on C. elegans and related nematodes isolated from the wild.
                display index
                fields natural_isolates
            </natural_isolates>
            <origin>
                name   origin
                title  Origin
                tooltip Origin of the strain.
                display report
                fields laboratory
                fields made_by
                fields contact
                fields date_received
                fields place
                fields gps_coordinates
                fields landscape
                fields substrate
                fields associated_organisms
                fields life_stage
                fields log_size_of_population
                fields sampled_by
                fields isolated_by
                fields date_isolated
            </origin>
            <phenotypes>
                name phenotypes
                title Phenotypes
                tooltip Phenotype of the strain, if described.
                display report
                precache true
                fields phenotypes
                fields phenotypes_not_observed
            </phenotypes>
            <references>
                name references
                title References
                display report
                tooltip References that cite or use this strain.
            </references>
        </widgets>
        <tools>
        </tools>
    </strain>

    <structure_data>
        title = Structure Data
        precache = true
        <browse>
        </browse>
        <search>
        </search>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview for this Structure Data
                display report
                fields name
                fields remarks
                fields sequence
                fields protein_homology
                fields homology_data
                fields status
            </overview>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                precache true
                fields  xrefs
            </external_links>
        </widgets>
        <tools>
        </tools>
    </structure_data>

    <transcript>
        title = Transcript
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
            fields = name
            fields = taxonomy
            fields = description
        </search>
        <default_widgets>
            overview
            sequences
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip An overview of the Transcript object.
                fields name
                fields taxonomy
                fields description
                fields sequence_type
                fields identity
                fields mature_product
                fields method
                fields remarks
                fields laboratory
                fields available_from
                fields corresponding_all
                fields feature
            </overview>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <location>
                name location
                title Location
                display report
                tooltip The genomic location of the Transcript.
                fields genomic_position
                fields genomic_image
                fields tracks
                fields genetic_position
            </location>
            <reagents>
                name reagents
                title Reagents
                display report
                tooltip Reagents related to the Transcript.
                fields microarray_assays
                fields orfeome_assays
                fields source_clone
                fields pcr_products
                fields matching_cdnas
            </reagents>
            <sequences>
                name sequences
                title Sequences
                display report
                tooltip Sequences and homologies.
    #             fields print_blast
                fields print_sequence
    #             fields print_homologies
                fields predicted_exon_structure
                fields predicted_units
    #            fields transcripts
                fields strand
            </sequences>
            <feature>
                name feature
                title Sequence features
                display report
                tooltip Sequence features associated with this transcript
                fields features
            </feature>
            <expression>
                name expression
                title Expression
                display report
                tooltip Expression patterns and data, including images from publications and time-lapse movies.
                fields anatomic_expression_patterns
                fields expression_profiling_graphs
                fields expression_patterns
                fields anatomy_terms
                fields expression_cluster
                fields fourd_expression_movies
                fields microarray_topology_map_position
                fields anatomy_function
             #   fields fpkm_expression_summary_ls # now load with ajax
            </expression>
        </widgets>
        <tools>
            nucleotide_aligner
        </tools>
    </transcript>

    <transgene>
        title = Transgene
        precache = true
        <browse>
            limits = Species
        </browse>
        <search>
            fields = name
            fields = summary
            fields = remarks
        </search>
        <default_widgets>
            overview
            isolation
        </default_widgets>
        <widgets>
            <tissue_specific_transgenes>
                name     tissue_specific_transgenes
                title    Tissue-specific
                tooltip  A list of known tissue-specific transgenes.
                display  index
                fields   tissue_specific_transgenes
            </tissue_specific_transgenes>
            <mapped_transgenes>
                name     mapped_transgenes
                title    Mapped
                tooltip  A list of known transgenes integrated into and mapped to the genome.
                display  index
                fields   mapped_transgenes
            </mapped_transgenes>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of this transgene.
                display report
                fields name
                fields taxonomy
                fields synonym
                fields summary
    # NEED TO ADD PUBLIC_NAME
                fields driven_by_gene
                fields fusion_reporter
                fields other_reporter
                fields remarks
                fields strains
                fields gene_product
                fields utr
                fields purification_tag
                fields recombination_site
                fields marked_rearrangement
                fields used_for
            </overview>
            <expr_pattern>
                name   expr_pattern
                title  Expression
                tooltip Expression details of this transgene.
                display report
                fields expression_patterns
                fields marker_for
            </expr_pattern>
            <human_diseases>
                name human_diseases
                title Human diseases
                display report
                fields detailed_disease_model
            </human_diseases>
            <isolation>
                name isolation
                title Construction details
                tooltip The construction details of this transgene.
                display report
                fields author
                fields construction_summary
                fields construct
                fields coinjection_marker
                fields coinjection_marker_other
                fields integrated_from
                fields laboratory
        # Disabled at curator request (K. Yook), 2011.03.18
        # fields clone
        # fields fragment
#               fields injected_into_strains -not in schema anymore -AC
                fields integration_method
                fields recombination_site
            </isolation>
            # The shared phenotypes* methods and phenotypes.tt2 widget.
            <phenotypes>
                name phenotypes
                title Phenotypes
                tooltip Phenotypes observed in animals carrying this transgene.
                display report
                fields phenotypes
                fields phenotypes_not_observed
            </phenotypes>
            <references>
                name references
                title References
                tooltip References that cite this transgene.
                display report
            </references>
        </widgets>
        <tools>
        </tools>
    </transgene>



    <transposon>
        title = Transposon
        precache = true
        <default_widgets>
            overview
            associations
            location
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of this transposon
                display report
                fields name
                fields taxonomy
                fields remarks
                fields old_name
                fields member_of
                fields copy_status
            </overview>
            <associations>
                name associations
                title Associations
                display report
                fields gene
                fields sequence
            </associations>
            <location>
                  name location
                  title Location
                  display report
                  tooltip The genomic location of the CDS.
                  fields genomic_position
                  fields genomic_image
                  fields tracks
                  fields genetic_position
            </location>
            <feature>
                name feature
                title Sequence features
                display report
                tooltip Sequence features associated with this transposon
                fields features
            </feature>
        </widgets>
        <tools>
        </tools>
    </transposon>


    <variation>
        title = Variation
        precache = true
        <browse>
            limits = Species
            limits = Gene_class
        </browse>
        <search>
          fields = name
          fields = taxonomy
          fields = status
          fields = variation_type
          fields = corresponding_gene
          fields = remarks
        </search>
        <layout>
          default = 02-456-10
        </layout>
        <widgets>
            <overview>
                name overview
                title Overview
                tooltip A concise overview of this variation.
                display report
                fields name
                fields other_names
                fields taxonomy
                fields variation_type
                fields corresponding_gene
                fields status
                fields remarks
              fields evidence
            </overview>
            <external_links>
                name    external_links
                title   External Links
                display report
                tooltip Links to third party resources.
                fields  xrefs
            </external_links>
            <genetics>
                name genetics
                title Genetics
                tooltip Genetic information about this variation, such as corresponding gene and other alleles.
                display report
                fields gene_class
                fields corresponding_gene
                fields reference_allele
                fields other_alleles
                fields linked_to
                fields strains
                fields rescued_by_transgene
            </genetics>
            <human_diseases>
                name human_diseases
                title Human diseases
                display report
                fields detailed_disease_model
            </human_diseases>
            <isolation>
                name   isolation
                title  Isolation
                tooltip Isolation history and details of the variation.
                display report
                fields laboratory
                fields external_source
                fields isolated_by_author
                fields isolated_by
        # fields source_database          # deprecated by xrefs
                fields date_isolated
                fields mutagen
                fields isolated_via_forward_genetics
                fields isolated_via_reverse_genetics
                fields transposon_excision
                fields transposon_insertion
                fields derived_from
                fields derivative
            </isolation>
            <location>
                name location
                title Location
                tooltip Genetic and genomic position of the variation.
                display report
                fields genomic_position
                fields genomic_image
                fields tracks
                fields genetic_position
            </location>
            <molecular_details>
                name molecular_details
                title Molecular Details
                tooltip Molecular details (if known) about the variation.
                display report
                fields variation_type
                fields sequencing_status
                fields nucleotide_change
                fields amino_acid_change
                fields cgh_deleted_probes
                fields cgh_flanking_probes
                fields flanking_pcr_products
                fields context
                fields deletion_verification
                fields features_affected
                fields detection_method
                fields affects_splice_site
                fields causes_frameshift
                fields polymorphism_type
                fields reference_strain
                fields polymorphism_status
                fields polymorphism_assays
            </molecular_details>
            <phenotypes>
                name phenotypes
                title Phenotypes
                tooltip Phenotype of the variation, if described.
                display report
# None of these fields are yet displayed. Uncomment once view is in place.
#                   fields nature_of_variation   # this doesn't belong here.
#                   fields dominance             # neither does this.
#                   fields phenotype_remark
# fields temperature_sensitivity
                fields phenotypes
                fields phenotypes_not_observed
            </phenotypes>
            <references>
                name references
                title References
                tooltip Publications that cite this variation.
                display report
            </references>
        </widgets>
        <tools>
        </tools>
    </variation>

    <pseudogene>
        display_in_dropdown yes
        title = Pseudogene
        <default_widgets>
            overview
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip pseudogene overview.
                fields parent_sequence
                fields taxonomy
                fields from_lab
                fields gene
                fields transposon
                fields brief_id
                fields type
                fields related_seqs
                fields remarks
            </overview>
            <expression>
                name expression
                title Expression
                display report
                tooltip Expression data
                fields microarray_results
            </expression>
            <genetics>
                name genetics
                title Genetics
                display report
                tooltip Genetic information such as alleles
                fields alleles
                fields polymorphisms
            </genetics>
            <reagents>
                name reagents
                title Reagent
                display report
                tooltip Experimental reagents.
                fields matching_cdnas
                fields sage_tags
            </reagents>
            <sequences>
                name sequences
                title Sequences
                display report
                tooltip Sequences
                fields print_sequence
                fields predicted_exon_structure
                fields strand
            </sequences>
            <feature>
                name feature
                title Sequence features
                display report
                tooltip Sequence features associated with this Pseudogene
                fields features
            </feature>
            <location>
                name location
                title Location
                display report
                tooltip Display the genetic and physical coordinates of the gene (if known).
                fields genomic_position
                fields genomic_image
                fields genetic_position
                fields tracks
            </location>
        </widgets>
        <tools>
        </tools>
    </pseudogene>

  </species>


  ######################################
  #
  # Resource pages.
  #
  ######################################

  <resources>
  title = Resources

    <analysis>
    title = Analysis
    precache = true
    <browse>
        limits = Title
    </browse>
    <search>
        fields = name
                fields = title
    </search>
    <default_widgets>
                 overview
        </default_widgets>
        <widgets>
        <overview>
            name   overview
            title  Overview
            tooltip Concise overview of this analysis.
            display report
            fields name
            fields description
            fields title
            fields based_on_wb_release
            fields based_on_db_release
            fields project
            fields subproject
            fields conducted_by
            fields url
        </overview>
        <external_links>
            name external_links
            title External Links
            display report
            tooltip Links to third party resources.
            fields xrefs
        </external_links>
        <references>
            name  references
            title References
            display report
            tooltip Publications that describe this analysis or method.
            </references>
    </widgets>
    <tools>
    </tools>
    </analysis>

    <gene_class>
      display_in_dropdown yes
    title = Gene class
    precache = true
    <browse>
        limits = Species
        limits = Gene_class
    </browse>
    <search>
        fields = name
        fields = description
    </search>
    <default_widgets>
        overview
        current_genes
    </default_widgets>
    <widgets>
#       <all_labs>
#           name     all_gene_classes
#           title    All Gene Classes
#           tooltip  A list of all gene classes tracked by Wormbase.
#           display  index
#           precache true
#           fields   all_gene_classes
#       </all_labs>
        <overview>
            name overview
            title Overview
            display report
            tooltip Gene class (eg Unc) overview.
            fields name
            fields other_names
            fields description
            fields laboratory
            fields former_laboratory
#                       fields phenotypes
            fields remarks
        </overview>
        <current_genes>
            name   current_genes
            title  Current Genes
            display report
            tooltip Genes currently placed in the current gene class.
            fields current_genes
        </current_genes>
        <previous_genes>
            name   previous_genes
            title  Previous Genes
            display report
            tooltip Genes that were once in the gene class but have since been reassigned.
            fields former_genes
            fields reassigned_genes
        </previous_genes>
    </widgets>
    <tools>
    </tools>
    </gene_class>

    # Can we display publications by laboratory?
    <laboratory>
      display_in_dropdown yes
    title = Laboratory
    precache = true
    <browse>
        limits = Title
    </browse>
    <search>
        fields = name
        fields = affiliation
        fields = representatives
        fields = strain_designation
        fields = allele_designation
    </search>
    <default_widgets>
        overview
        members
    </default_widgets>
    <widgets>
        <all_labs>
            name     all_labs
            title    All Labs
            tooltip  A list of all laboratories registered with WormBase and the Caenorhabditis Geetic Center (CGC).
            display  index
            fields   all_labs
        </all_labs>
        <overview>
            name   overview
            title  Overview
            tooltip A concise overview of this laboratory.
            display report
            fields name
            fields affiliation
            fields representatives
            fields website
            fields email
            fields strain_designation
            fields allele_designation
            fields remarks
        </overview>
        <members>
            name   members
            title  Lab Members
            tooltip Current and former members of this laboratory.
            display report
            fields current_members
            fields former_members
        </members>
        <gene_classes>
            name gene_classes
            title Gene Classes
            display report
            tooltip Gene classes under the purview of this laboratory.
            fields gene_classes
            fields former_gene_classes
        </gene_classes>
        <alleles>
            name   alleles
            title  Alleles
            display report
            tooltip Alleles generated by this laboratory.
            fields alleles
        </alleles>
        <strains>
            name strains
            title Strains
            display report
            tooltip Strains generated by -- and possibly available from -- this laboratory.
            fields strains
        </strains>
    </widgets>
    <tools>
        </tools>
    </laboratory>


    <molecule>
    title = Molecule
    precache = true
    <browse>
    </browse>
    <search>
    </search>
    <default_widgets>
        overview
        affected
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            tooltip A concise overview for this molecule.
            display report
            fields name
            fields synonyms
            fields inchi
            fields inchi_key
            fields smiles
            fields formula
            fields iupac
            fields monoisotopic_mass
            fields molecule_use
            fields biological_role
            fields biofunction_role
            fields detection_status
            fields detection_method
            fields extraction_method
            fields nonspecies_source
            fields chebi_id
            fields remarks
        </overview>
        <affected>
            name affected
            title Genes Affected
            tooltip Genes affected by this molecule.
            display report
#            fields affected_variations
#            fields affected_transgenes
            fields affected_genes
#            fields affected_rnai
        </affected>
        <strains>
            name strains
            title Strains Affected
            tooltip Strains Affected
            display report
            fields affected_strains
        </strains>
        <structure>
            name structure
            title Structure
            tooltip Structure
            display report
            fields inchi
            fields inchi_key
            fields smiles
            fields formula
            fields iupac
            fields monoisotopic_mass
        </structure>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to third party resources.
            fields  xrefs
        </external_links>
        <references>
            name references
            title References
            display report
            fields references
        </references>
    </widgets>
    <tools>
    </tools>
    </molecule>


   <motif>
        display_in_dropdown yes
    title = Motif
        precache = true
    <browse>
        limits = Species
        limits = Motif
        </browse>
    <search>
        fields = name
        fields = title
        fields = remarks
        </search>
    <default_widgets>
        overview
        </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            display report
            tooltip An overview of the motif.
            fields name
            fields title
            fields remarks
            fields gene_ontology
            fields homologies
        </overview>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to external third party resources.
            fields  xrefs
        </external_links>
    </widgets>
        <tools>
        </tools>
    </motif>

    <paper>
        display_in_dropdown yes
    title = Paper
    precache = true
    <browse>
        limits = Title
    </browse>
    <search>
        fields authors
        fields title
        fields abstract
        fields year
        fields journal
        fields volume
        fields pages
            fields name
    </search>
    <default_widgets>
        overview
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            tooltip A concise overview of this paper.
            display report
            fields name
            fields authors
            fields title
            fields editors
            fields abstract
            fields remarks
            fields year
            fields journal
            fields volume
            fields pages
            fields keywords
            fields publisher
            fields affiliation
            fields pmid
            fields doi
            fields intext_citation
            fields publication_type
            fields is_wormbook_paper
            fields remarks
            fields status
            fields merged_into
        </overview>
        <referenced>
            name referenced
            title Referenced
            tooltip Entities referenced by this paper.
            fields refers_to
            display report
        </referenced>
        # add back for WS245
        # <related_papers>
        #   name related_papers
        #   title Related Papers
        #   fields pmid
        #   fields doi
        #   tooltip Other related papers.
        #   display report
        # </related_papers>
        <external_links>
            name external_links
            title External Links
            display report
            tooltip Links to third party resources.
            fields xrefs
        </external_links>
            <history>
        name history
                title History
                display report
                tooltip WormBase curatorial history for the gene.
                fields history_lite
            </history>
    </widgets>
    <tools>
    </tools>

    #HACK I need this for sorting paper types. I'm sorry. -AC (You owe us some TimBits -WormBase Team)
    <paper_types>
      Journal_article = 0
      Review = 1
      Comment = 2
      News = 3
      Letter = 4
      Editorial = 5
      Congresses = 6
      Historical_article = 7
      Biography = 8
      Interview = 9
      Lectures = 10
      Interactive_tutorial = 11
      Retracted_publication = 12
      Technical_report = 13
      Directory = 14
      Monograph = 15
      Published_erratum = 16
      Meeting_abstract = 17
      Gazette_article = 18
      Book_chapter = 19
      Book = 20
      Email = 21
      WormBook = 22
      Other= 23
    </paper_types>
    </paper>


    # The Person Summary
    # TH, 2011.05.24: Complete.
    # Publications needs better formatting (is Abby's paper with abstract drop-in?)
    # Needs custom search
    <person>
      display_in_dropdown yes
    title = Person
    precache = true
    <browse>
        limits = Title
    </browse>
    <search>
        fields = name
        fields = institution
#                fields = strain_designation
#                fields = allele_designation
    </search>
    <default_widgets>
        overview
        laboratory
    </default_widgets>
    <widgets>
        <overview>
            name   overview
            title  Overview
            tooltip General contact information for this person.
            display report
            fields name
            fields street_address
            fields country
            fields institution
            fields email
            fields aka
            fields orcid
            # fields lab_phone
            # fields office_phone
            # fields fax
            fields web_page
            fields previous_addresses
            fields lab_representative_for
        </overview>
        <laboratory>
            name   laboratory
            title  Lab Affiliation
            tooltip Laboratory affiliation for this person.
            display report
            fields laboratory
            fields lab_info
            fields gene_classes
            fields previous_laboratories
        </laboratory>
        <lineage>
            name   lineage
            title  Lineage
            tooltip Intellectual lineage, including people that this person has worked with or for.
            display report
            fields ancestors_data
            fields supervised
            fields supervised_by
            fields worked_with
        </lineage>
        # This needs some TLC or to be replaced wholesale.
        <publications>
            name  publications
            title Publications
            tooltip Publications by or citing this person.
            display report
            fields publications
            fields meeting_abstracts
        </publications>
        <tracking>
            name   tracking
            title  Tracking
            tooltip Internal WormBase tracking information.
            display report
            fields status
            fields possibly_publishes_as
            fields last_verified
        </tracking>
    </widgets>
    <tools>
    </tools>
    </person>

    # Not handled yet.
     <picture>
        title Picture
        <widgets>
            <lightbox>
                name lightbox
                title Overview
                display report
                fields name
                fields description
                fields remarks
                fields reference
                fields contact
                # xref pictures
                fields cropped_from
                fields cropped_pictures
                # image data
                fields image
                fields external_source
                # stuff depicted
                fields expression_patterns
                fields go_terms
                fields anatomy_terms
            </lightbox>
        </widgets>
        <tools>
        </tools>
    </picture>


    # The static "Find Reagents" page
    # Not handled yet.
    # 2012.04.21: Is this still in use? - TH
    <reagents>
        title = Reagent
        display_in_dropdown yes
        static = true
        <default_widgets>
                strains
        </default_widgets>
        <widgets>
                <strains>
                    name strains
                    title Strains
                    display report
                </strains>
                <clones>
                    name clones
                    title Clones
                    display report
                </clones>
                <equipment>
                    name equipment
                    title Equipment
                    display report
                </equipment>
                <rnai_libraries>
                    name rnai_libraries
                    title RNAi Libraries
                    display report
                </rnai_libraries>
            <microarrays>
                    name microarrays
                    title Microarrays
                    display report
                </microarrays>
            </widgets>
    </reagents>

    # The Disease Summary Page

    <disease>
      display_in_dropdown yes
    title = Disease Ontology
    <default_widgets>
        overview
    </default_widgets>
    <widgets>
        <overview>
            name overview
            title Overview
            display report
            tooltip disease overview.
            fields name
            fields definition
            fields omim
            fields status
            fields remarks
            fields parent
            fields child
            fields type
            fields synonym
            fields genes_orthology
            fields genes_biology
        </overview>
        <external_links>
            name    external_links
            title   External Links
            display report
            tooltip Links to third party resources.
            fields  xrefs
        </external_links>
        <ontology_browser>
            name ontology_browser
            title Ontology Browser
            tooltip Disease Term Browser
            display report
            fields name
        </ontology_browser>
    </widgets>
    <tools>
    </tools>
    </disease>

    <transposon_family>
        display_in_dropdown yes
        title = Transposon Family
        <default_widgets>
            overview

        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip pseudogene overview.
                fields title
                fields description
                fields remarks
            </overview>
            <transposons>
                name transposons
                title Family Members
                display report
                tooltip transposons in this family
                fields family_members
            </transposons>
            <var_motifs>
                name var_motifs
                title Variations and Motifs
                display report
                tooltip Variations and motifs attached to this record.
                fields variations
                fields motifs
            </var_motifs>
        </widgets>
    </transposon_family>



    <wbprocess>
        display_in_dropdown yes
        title = Process&Pathway
        <default_widgets>
            overview
            entities
        </default_widgets>
        <widgets>
            <overview>
                name overview
                title Overview
                display report
                tooltip disease overview.
                fields name
                fields summary
                fields related_process
                fields other_name
        fields historical_gene
        fields life_stage
            </overview>
            <anatomy>
                name anatomy
                title Anatomy
                display report
                fields anatomy_term
            </anatomy>
            <genes>
                name genes
                title Genes
                display report
                fields genes
            </genes>
            <expression_clusters>
                name expression_clusters
                title Expression Clusters
                display report
                fields expression_cluster
            </expression_clusters>
            <interactions>
                name interactions
                title Interactions
                display report
                fields interactions
            </interactions>
            <go_term>
                name go_term
                title Gene Ontology
                display report
                fields go_term
            </go_term>
            <phenotypes>
                name phenotypes
                title Phenotypes
                display report
                fields phenotypes
            </phenotypes>
            <molecule>
                name molecule
                title Molecule
                display report
                fields molecules
            </molecule>
            <references>
                name references
                title References
                display report
                fields reference
            </references>
            <pathways>
                name pathways
                title Pathways
                display report
                fields pathway
            </pathways>
        </widgets>
        <tools>
        </tools>

    </wbprocess>

  </resources>



  ######################################
  #
  # Tools.
  #
  ######################################

  <tools>
    title = Tools
    <gbrowse>
        title  = GBrowse
        display = report
        url = /tools/genome/gbrowse/c_elegans
        display_in_dropdown yes
    </gbrowse>
    <jbrowse>
        title  = JBrowse
        display = report
        url = /tools/genome/jbrowse-simple/?data=data/c_elegans_PRJNA13758
        display_in_dropdown yes
    </jbrowse>
    <synteny>
        title  = Synteny
        display = report
        url = /tools/synteny/mercator
    </synteny>
    <wormmine>
        title  = WormMine
        url = http://intermine.wormbase.org
        display = report
        display_in_dropdown yes
    </wormmine>
    <simplemine>
        title  = SimpleMine
        url = http://www.wormbase.org/tools/mine/simplemine.cgi
        display = report
        display_in_dropdown yes
    </simplemine>
    <parasite_biomart>
        title = ParaSite BioMart
        url = http://parasite.wormbase.org/biomart/martview/
        display = report
        display_in_dropdown yes
    </parasite_biomart>
    <blast_blat>
        title  = Blast/Blat
        display = report
        display_in_dropdown yes
    </blast_blat>
    <downloads>
        title  = Downloads
        url = ftp://ftp.wormbase.org/pub/wormbase/
        display = report
    </downloads>
    <epcr>
    name = epcr
        title  = e-PCR
    tooltip = e-PCR Search
        display = report
    </epcr>
    <epic>
    name = epic
        title  = ACeDB Image
    tooltip = ACeDB Graphic Display
        display = both
    </epic>
    <gmap>
    name = gmap
        title  = Genetic Map
    tooltip = ACeDB Genetic Map Display
        display = report
    </gmap>
#    <nearby_genes>
#	name = nearby_genes
#        title  = Nearby Genes
#	tooltip = Genes near the currently selected gene.
#        display = report
#        display_in_dropdown yes
#    </nearby_genes>
    <protein_aligner>
        name    = protein_aligner
        title   = Protein Aligner
        tooltip = Protein Aligner
        display = both
    </protein_aligner>
    <nucleotide_aligner>
        name    = nucleotide_aligner
        title   = Nucl. Aligner
        tooltip = Nucleotide Aligner
        display = both
    </nucleotide_aligner>
    <issues>
        title  = Contact Help
        url = /tools/support
        display = both
    </issues>
    <comments>
        title = Comments
        display = both
    </comments>
    <tree>
        name    = tree
        title   = Tree Display
        tooltip = View the raw data for this object or explore the underlying data model.
        display = both
    </tree>
    <schema>
        name    = schema
        title   = Schema
        tooltip = Explore the underlying data model of the object.
        display = both
    </schema>
    <spell>
        name    = spell
        title   = SPELL
        url     = https://spell.wormbase.org
        tooltip = WormBase SPELL instance
    </spell>
    <queries>
        title   = Queries
        tooltip = Make AQL/WQL queries directly
    </queries>
    <textpresso>
        title = Textpresso
        url = http://www.textpresso.org/celegans/
    </textpresso>
    <ontology_browser>
    title = Ontologies
        display_in_dropdown yes
    <terms>
         anatomy_term = Anatomy Ontology
         go_term      = Gene Ontology
         phenotype    = Phenotype
    </terms>
    </ontology_browser>
  </tools>


  ######################################
  #
  # Me.
  #
  ######################################

  <me>
      <widgets>
        <favorites>
          name favorites
          title My Favorites
        </favorites>
        <user_history>
          name user_history
          title My History
        </user_history>
        <profile>
          name profile
          title My Profile
          login = 1
        </profile>
        <my_library>
          name my_library
          title My Library
        </my_library>
      </widgets>
  </me>


<species_list>

  # All is a special type of species.
  # Configuration included here for easily building the species index page.
  # These config is post-processed by lib/WormBase/Web.pm .
  <all>
      title All Species
      display_in_dropdown yes
      gbrowse             no
      gene_models         no
      notes
      <default_widgets>
                 overview
         downloads
      </default_widgets>
      <widgets>
#           <overview>
#               name overview
#               title Overview
#           </overview>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
      </widgets>
      # These are the classes available from the drop down menu
      <available_classes>
           class antibody
           class expression_cluster
           class life_stage
           class gene
           class gene_class
           class phenotype
           class protein
           class sequence
           class strain
           class transgene
           class variation
       </available_classes>
  </all>


    <a_ceylanicum>
       title A. ceylanicum
       genus Ancylostoma
       species ceylanicum
       ncbi_taxonomy_id 53326
       common_name hookworm
       tier                    III
       display_in_dropdown     no
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJNA231479>
           title  BioProject PRJNA231479
         </PRJNA231479>
       </bioprojects>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </a_ceylanicum>

   <a_suum>
       title A. suum
       genus Ascaris
       species suum
       ncbi_taxonomy_id 6253
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA80881>
           title  BioProject PRJNA80881
           cannonical 1
         </PRJNA80881>
         <PRJNA62057>
           title  BioProject PRJNA62057 (Davis assembly)
         </PRJNA62057>
       </bioprojects>
       <source>
          name University of Melbourne; BGI
          url
          contact Aaron Jex
          email ajex@unimelb.edu.au
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </a_suum>

    <b_malayi>
      title B. malayi
      genus Brugia
      species malayi
      common_name agent of lymphatic filariasis
      ncbi_taxonomy_id 6279
      current_version
      tier                    III
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
       <bioprojects>
         <PRJNA10729>
           title  BioProject PRJNA10729
         </PRJNA10729>
       </bioprojects>
      <gff_availability>
          gff2
      </gff_availability>
      <source>
          name TIGR -> WashU/Sanger
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
            # These are the classes available from the drop down menu
      <available_classes>
           class cds
           class feature
           class gene
           class operon
           class protein
           class sequence
           class strain
           class transcript
      </available_classes>
    </b_malayi>

    <b_xylophilus>
      title B. xylophilus
      genus Bursaphelenchus
      species xylophilus
      common_name pine wood nematode
      ncbi_taxonomy_id 6326
      current_version
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJEA64437>
          title  BioProject PRJEA64437
        </PRJEA64437>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
            class gene
            class protein
            class sequence
            class strain
      </available_classes>
    </b_xylophilus>

    <c_angaria>
      title C. angaria
      genus Caenorhabditis
      species angaria
      common_name
      ncbi_taxonomy_id        96668
      current_version
      tier                    II
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA51225>
          title  BioProject PRJNA51225
        </PRJNA51225>
      </bioprojects>
      <source>
          name Caltech
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </c_angaria>

    <c_elegans>
      title C. elegans
      genus Caenorhabditis
      species elegans
      common_name
      ncbi_taxonomy_id 6239
      current_version
      tier            I
      display_in_dropdown yes
      gbrowse             yes
      gene_models         yes
      <bioprojects>
        <PRJNA13758>
          title  BioProject PRJNA13758
        </PRJNA13758>
      </bioprojects>
      <gff_availability>
          gff2
      </gff_availability>
      <source>
          name
          url
          contact
          email
      </source>
      notes
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      # These are the classes available from the drop down menu
      <available_classes>
           class cds
           class clone
           class expression_cluster
           class feature
           class gene
           class microarray_results
           class operon
           class pcr_oligo
           class protein
           class rearrangement
           class rnai
           class sequence
           class strain
           class transcript
           class transgene
           class transposon
           class variation
       </available_classes>
    </c_elegans>

   <c_elegans_PRJNA275000>
      title C. elegans CB4856
      genus Caenorhabditis
      species elegans
      strain CB4856
      common_name
      ncbi_taxonomy_id 6239
      current_version
      tier            III
      display_in_dropdown no
      gbrowse             yes
      gene_models         yes
      <bioprojects>
        <PRJNA275000>
          title  BioProject PRJNA275000
        </PRJNA275000>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      notes
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      # These are the classes available from the drop down menu
      <available_classes>
      </available_classes>
    </c_elegans_PRJNA275000>


   <c_elegans_PRJEB28388>
      title C. elegans VC2010
      genus Caenorhabditis
      species elegans
      strain VC2010
      common_name
      ncbi_taxonomy_id 6239
      current_version
      tier            III
      display_in_dropdown no
      gbrowse             yes
      gene_models         yes
      <bioprojects>
        <PRJEB28388>
          title  BioProject PRJEB28388
        </PRJEB28388>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      notes
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      # These are the classes available from the drop down menu
      <available_classes>
      </available_classes>
    </c_elegans_PRJEB28388>


    <c_brenneri>
      title C. brenneri
      genus Caenorhabditis
      species brenneri
      common_name =
      ncbi_taxonomy_id 135651
      current_version
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA20035>
          title  BioProject PRJNA20035
        </PRJNA20035>
      </bioprojects>
      <source>
          name WashU
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
       </available_classes>
    </c_brenneri>

    <c_briggsae>
      title C. briggsae
      genus Caenorhabditis
      species briggsae
      common_name =
      ncbi_taxonomy_id 6238
      current_version CB4
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA10731>
          title  BioProject PRJNA10731
        </PRJNA10731>
      </bioprojects>
      <source>
          name WashU
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
           class feature
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
           class transgene
           class variation
       </available_classes>
    </c_briggsae>

   <c_inopinata>
      title C. inopinata
      genus Caenorhabditis
      species inopinata
      common_name =
      ncbi_taxonomy_id 1978547
      current_version
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJDB5687>
          title  BioProject PRJDB5687
        </PRJDB5687>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
              fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </c_inopinata>

   <c_japonica>
      title C. japonica
      genus Caenorhabditis
      species japonica
      common_name =
      ncbi_taxonomy_id 281687
      current_version
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA12591>
          title  BioProject PRJNA12591
        </PRJNA12591>
      </bioprojects>
      <source>
          name WashU
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
           class variation
       </available_classes>
    </c_japonica>

   <c_latens>
      title C. latens
      genus Caenorhabditis
      species latens
      common_name =
      ncbi_taxonomy_id 1503980
      current_version
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA248912>
          title  BioProject PRJNA248912
        </PRJNA248912>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
              fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </c_latens>

   <c_nigoni>
      title C. nigoni
      genus Caenorhabditis
      species nigoni
      common_name =
      ncbi_taxonomy_id 1611254
      current_version
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA384657>
          title  BioProject PRJNA384657
        </PRJNA384657>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
              fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </c_nigoni>

    <c_remanei>
       title C. remanei
       genus Caenorhabditis
       species remanei
       common_name =
       ncbi_taxonomy_id 31234
       current_version
       tier                    II
       display_in_dropdown     yes
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA53967>
           title  BioProject PRJNA53967
         </PRJNA53967>
       </bioprojects>
       <source>
          name WashU
          url
          contact
          email
      </source>

      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
     <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
      </available_classes>
    </c_remanei>

    <c_remanei_PRJNA248909>
       title C. remanei PX356
       genus Caenorhabditis
       species remanei
       strain  PX356
       common_name =
       ncbi_taxonomy_id 31234
       current_version
       tier                    II
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA248909>
           title  BioProject PRJNA248909
         </PRJNA248909>
       </bioprojects>
       <source>
          name WashU
          url
          contact
          email
      </source>

      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
     <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
      </available_classes>
    </c_remanei_PRJNA248909>

    <c_remanei_PRJNA248911>
       title C. remanei PX439
       genus Caenorhabditis
       species remanei
       strain  PX439
       common_name =
       ncbi_taxonomy_id 31234
       current_version
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA248911>
           title  BioProject PRJNA248911
         </PRJNA248911>
       </bioprojects>
       <source>
          name WashU
          url
          contact
          email
      </source>

      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
     <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
      </available_classes>
    </c_remanei_PRJNA248911>

    <c_sinica>
       title C. sinica
       genus Caenorhabditis
       species "sinica"
       ncbi_taxonomy_id        497871
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             no
       <bioprojects>
         <PRJNA194557>
           title  BioProject PRJNA194557
         </PRJNA194557>
       </bioprojects>
       <source>
          name Sanger
          url
          contact
          email
       </source>
       notes
       <default_widgets>
         overview
         downloads
         assemblies
       </default_widgets>
       <widgets>
       # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
       </widgets>
       <available_classes>
            class gene
       </available_classes>
    </c_sinica>

    <c_tropicalis>
       title C. tropicalis
       genus Caenorhabditis
       species tropicalis
       ncbi_taxonomy_id 886184
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA53597>
           title  BioProject PRJNA53597
         </PRJNA53597>
       </bioprojects>
       <source>
          name Sanger
          url
          contact
          email
      </source>
      notes
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
            class gene
      </available_classes>
    </c_tropicalis>

    <d_immitis>
      title D. immitis
      genus Dirofilaria
      species immitis
      ncbi_taxonomy_id 6287
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJEB1797>
          title  BioProject PRJEB1797
        </PRJEB1797>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
        fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </d_immitis>


    <h_bacteriophora>
       title H. bacteriophora
       genus Heterorhabditis
       species bacteriophora
       common_name =
       ncbi_taxonomy_id 37862
       current_version
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             no
       <bioprojects>
         <PRJNA13977>
           title  BioProject PRJNA13977
         </PRJNA13977>
       </bioprojects>
       <source>
          name WashU
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
     <available_classes>
        class gene
        class protein
        class sequence
        class strain
     </available_classes>
    </h_bacteriophora>

    <h_contortus>
       title H. contortus
       genus Haemonchus
       species contortus
       common_name barber pole worm
       ncbi_taxonomy_id 6289
       current_version
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJEB506>
           title  BioProject PRJEB506
         </PRJEB506>
         <PRJNA205202>
           title  BioProject PRJNA205202
         </PRJNA205202>
       </bioprojects>
       <source>
          name Sanger
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </h_contortus>

    <l_loa>
      title L. loa
      genus Loa
      species loa
      common_name  eye worm
      ncbi_taxonomy_id 7209
      current_version V3
      tier            III
      display_in_dropdown no
      gbrowse             yes
      gene_models         yes
      <bioprojects>
        <PRJNA60051>
          title  BioProject PRJNA60051
        </PRJNA60051>
      </bioprojects>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </l_loa>

    <m_hapla>
      title M. hapla
      genus Meloidogyne
      species hapla
      common_name =
      ncbi_taxonomy_id 6305
       tier                    III
       display_in_dropdown     no
       gbrowse                 yes
       gene_models             yes
       <bioprojects>
         <PRJNA29083>
           title  BioProject PRJNA29083
         </PRJNA29083>
       </bioprojects>
       <source>
          name NCSU
          url hapla.org
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class protein
        class sequence
        class strain
      </available_classes>
    </m_hapla>

    <m_incognita>
      title M. incognita
      genus Meloidogyne
      species incognita
      common_name southern root-knot nematode
      ncbi_taxonomy_id 6306
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             no
      <bioprojects>
        <PRJEA28837>
          title  BioProject PRJEA28837
        </PRJEA28837>
      </bioprojects>
      <source>
          name INRA
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class protein
        class sequence
        class strain
      </available_classes>
    </m_incognita>


    <n_americanus>
       title N. americanus
       genus Necator
       species americanus
       ncbi_taxonomy_id 51031
       tier                    III
       display_in_dropdown     no
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJNA72135>
           title  BioProject PRJNA72135
         </PRJNA72135>
       </bioprojects>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </n_americanus>

   <o_tipulae>
      title O. tipulae
      genus Oscheius
      species tipulae
      common_name =
      ncbi_taxonomy_id
      current_version
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJEB15512>
          title  BioProject PRJEB15512
        </PRJEB15512>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
              fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </o_tipulae>

   <o_volvulus>
      title O. volvulus
      genus Onchocerca
      species volvulus
      ncbi_taxonomy_id 6282
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJEB513>
          title  BioProject PRJEB513
        </PRJEB513>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
#           class expression_cluster
           class gene
#           class microarray_results
#           class pcr_oligo
           class protein
           class sequence
#           class strain
           class transcript
           class feature
       </available_classes>
    </o_volvulus>


    <p_exspectatus>
       title P. exspectatus
       genus Pristionchus
       species exspectatus
       ncbi_taxonomy_id 1195656
       tier                    III
       display_in_dropdown     no
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJEB6009>
           title  BioProject PRJEB6009
         </PRJEB6009>
       </bioprojects>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </p_exspectatus>

   <p_pacificus>
      title P. pacificus
      genus Pristionchus
      species pacificus
      ncbi_taxonomy_id 54126
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA12644>
          title  BioProject PRJNA12644
        </PRJNA12644>
      </bioprojects>
      <source>
          name WashU/MPI
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
           class expression_cluster
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
       </available_classes>
    </p_pacificus>

   <p_redivivus>
      title P. redivivus
      genus Panagrellus
      species redivivus
      ncbi_taxonomy_id 6233
      tier                    III
      display_in_dropdown     no
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJNA186477>
          title  BioProject PRJNA186477
        </PRJNA186477>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
      </default_widgets>
      <widgets>
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
        fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
       </available_classes>
    </p_redivivus>

   <s_ratti>
      title S. ratti
      genus Strongyloides
      species ratti
      ncbi_taxonomy_id 34506
       tier                    III
       display_in_dropdown     yes
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJEB125>
           title  BioProject PRJEB125
         </PRJEB125>
       </bioprojects>
       <source>
          name Sanger
          url
          contact
          email
      </source>
      notes 30 June 2010: Assembly due out in mid 2011. They have fosmid & BAC libraries. Have ~5000 contigs and ~99% of genome done. Have about 10,000 genes which is the expected number as it is half the size of C. elegans.
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </s_ratti>

    <t_spiralis>
       title T. spiralis
       genus Trichinella
       species spiralis
       ncbi_taxonomy_id 6334
       tier                    III
       display_in_dropdown     no
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJNA12603>
           title  BioProject PRJNA12603
         </PRJNA12603>
       </bioprojects>
       <source>
          name WashU
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
        class gene
        class protein
        class sequence
        class strain
      </available_classes>
    </t_spiralis>

    <t_suis>
       title T. suis
       genus Trichuris
       species suis
       ncbi_taxonomy_id 68888
       tier                    III
       display_in_dropdown     no
       common_name pig whipworm
       gbrowse                 no
       gene_models             no
       <bioprojects>
         <PRJNA208415>
           title  BioProject PRJNA208415
         </PRJNA208415>
        <PRJNA208416>
           title  BioProject PRJNA208416
         </PRJNA208416>
       </bioprojects>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
          fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
      </available_classes>
    </t_suis>

   <t_muris>
      title T. muris
      genus Trichuris
      species muris
      common_name =
      ncbi_taxonomy_id 70415
      current_version
      tier                    II
      display_in_dropdown     yes
      gbrowse                 yes
      gene_models             yes
      <bioprojects>
        <PRJEB126>
          title  BioProject PRJEB126
        </PRJEB126>
      </bioprojects>
      <source>
          name
          url
          contact
          email
      </source>
      <default_widgets>
         overview
         downloads
         assemblies
      </default_widgets>
      <widgets>
      # Built programmatically. This cannot be a custom widget.
          <downloads>
              name   downloads
              title  Downloads
          </downloads>
          <assemblies>
              name   assemblies
              title  Genome Assemblies
              fields current_assemblies
              fields previous_assemblies
          </assemblies>
      </widgets>
      <available_classes>
           class cds
           class gene
           class microarray_results
           class pcr_oligo
           class protein
           class sequence
           class strain
           class transcript
           class variation
       </available_classes>
    </t_muris>

</species_list>

# parasite configs are set dynamically in lib/WormBase/Web.pm
# based on result of traversing ftp site
parasite_species_list = 0

############################
#
#  submit data navbar option
#
############################
<submit_data>
    title Submit data
    url about/userguide/submit_data
    <phenotypes>
        title Phenotypes
        display_in_dropdown     yes
        url http://www.wormbase.org/submissions/phenotype.cgi
    </phenotypes>
    <z_more>
        title More...
        display_in_dropdown     yes
        url /about/userguide/submit_data
    </z_more>
</submit_data>

</sections>


##################################################################
#
#  URIs of external resources
# Shouldn't these be part of the view?
#
##################################################################



# ONLY USED IN ONE PLACE: classes/phenotype/ontology_browser.tt2
<external_url>
        tree_lister = http://dev.wormbase.org/db/ontology/tree_lister?name=
             aligner = http://www.wormbase.org/db/seq/aligner?
          blast_blat = http://www.wormbase.org/db/searches/blast_blat
    genomic_location = http://www.wormbase.org/db/gb2/gbrowse/?
       gbrowse_image = http://www.wormbase.org/db/gb2/gbrowse_img/
#        PHOSPHOPEP = http://www.sbeams.org/dev1/sbeams/cgi/Glycopeptide/peptideSearch.cgi?action=Show_hits_form&search_type=accession&organism=cel&search_term=%s
WORFDB      =  http://worfdb.dfci.harvard.edu/index.php?page=race
WIKI         = http://wiki.wormbase.org/index.php/%s
BLAST        = /db/searches/blast_blat

</external_url>


# Choosing which template to render:
# 1. Common: Is the field/widget listed in the common_* hash? Use it.
# 2. Custom: Is the field/widget listed in the custom_* hash? Use it.
# 3. Fall back to generic field/widget

# BETTER YET:
# 1. Does a common template exist for this field? Use it.
# 2. Does a custom template exist for this field? Use it.
# 3. Otherwise, use a generic template.

# common_fields are used throughout the model and do not
# belong to a specific class but still require custom templates.
# If your model requires one of these fields, all you need to do
# is specify it in your configuration.
<common_fields>
    alleles = 1
    interaction_details = 1
    genomic_position = 1
        genomic_environs = 1
        history = 1
    phenotypes_observed = 1
    phenotypes_not_observed = 1
    polymorphisms = 1
    references = 1
    strains = 1
    fpkm_expression_summary_ls = 1
</common_fields>

# Common widgets, shared across models.
# Is this still in use? Yes
<common_widgets>
    external_links = 1
    history        = 1
    location       = 1
    phenotypes     = 1
    references     = 1
    ontology_browser =1
    interactions   = 1
    expression     = 1
    feature        = 1
    human_diseases = 1
</common_widgets>