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# important info:
# grep ??? access.log.?
# find GET
# cd /data/reports/reports_db/output
# foreach i (*.rpt)
# ls -l $i
# grep $i /logs/www/newGondor/access.log.2023.12.11 | grep GET
# bhmgiapp01:/logs/www/newGondor => nslookup 10.3.0.185
# 185.0.3.10.in-addr.arpa name = bhsqldb06wp.jax.org.
#
# mgimarkerfeed
# It is used in the MGI staging feed, which is triggered every day when JaxStrain ETL is run.
# Scott Rizzo <Scott.Rizzo@jax.org>
#
# these reports are no longer being created, but ouput files still exist.
# so, do NOT remove these files
# bhmgiapp01:/data/reports/reports_db/output
# MGI_GTdbGSS_info.rpt
# MGI_GTDNA.rpt
# MGI_GTGUP.rpt
# MGI_GTRNA.rpt
#
TAG: reports_db-6-0-27-4
DATE: 03/10/2026
STAFF: pf
wts2-1391/HP-MP Lexical Matches report
new: weekly/MGI_HpMpLexical.py
TAG: reports_db-6-0-27-3
DATE: 01/28/2026
STAFF: lec
wts2-1793/sprt-204/add genotype IDs to reports with genotypes
modified: index.shtml
modified: weekly/MGI_GenePheno.py
modified: weekly/MGI_PhenoGenoMP.py
TAG: reports_db-6-0-27-2
DATE: 01/22/2026
STAFF: jer
wts2-1792/sprt-202/Report that lists all MP terms associated with an allele
added: ALL_Phenotype.py
updated: index.shtml
TAG: reports_db-6-0-27-1
DATE: 01/21/2026
STAFF: lec
wts2-1790/sprt-201/genotypes missing from MGI_Geno_DiseaseDO.rpt public report
modified: MGI_GenePheno.py
TAG: reports_db-6-0-26-6
DATE: 12/16/2025
STAFF: lec
wts2-1778/sprt-161/Remove Obsolete Public, QC Reports
deleted: daily/MGI_Cov_Allele.py
deleted: daily/MGI_Cov_Human_Gene.py
deleted: daily/MGI_Cov_Mouse_Gene.py
deleted: daily/MGI_Cov_Strain.py
TAG: reports_db-6-0-26-5
DATE: 12/12/2025
STAFF: lec
wts2-1771/sprt-153/MGI GPI missing GCRPs as cross reference
modified: GO_gpi.py
TAG: reports_db-6-0-26-4
DATE: 12/02/2025
STAFF: lec
wts2-1764/sprt-143/Update to MGI GPI File
remove all lines that begin with the following identifiers in the first column of the MGI GPI file:
EMBL:
RefSeq:
ENSEMBL:
modified: GO_gpi.py
TAG: reports_db-6-0-26-3
DATE: 10/21/2025
STAFF: lec
wts2-1710/sprt-100/NCBI reported having difficullty downloading the MGI logo icon from our Linkout file
modified: Configuration.default
modified: ncbilinkout/nucleotide_linkout.py
modified: ncbilinkout/protein_linkout.py
modified: ncbilinkout/pubmed_linkout.py
remove:
<!ENTITY icon https://www.informatics.jax.org/mgihome/homepages/images/MGILinkout.jpg>
<IconUrl>&icon;</IconUrl>
TAG: reports_db-6-0-26-2
TAG: reports_db-6-0-26-1
DATE: 09/17/2025
STAFF: lec
wts2-1725/sprt-59/inconsistencies between MGI GPI and GOA_mouse GPI
modified: daily/GO_gpi.py
TAG: reports_db-6-0-25-8
DATE: 06/10/2025
STAFF: lec
wts2-1677/e4g-282/NCBI Linkout Reports - update URLs
modified: Configuration.default
modified: ncbilinkout/copy_rpt.csh
modified: ncbilinkout/ncbilinkout.csh
modified: ncbilinkout/providerinfo.xml
TAG: reports_db-6-0-25-7
DATE: 06/02/2025
STAFF: lec
wts2-1669/e4g-264/Python 3.12
TAG: reports_db-6-0-25-6
DATE: 05/15/2025
STAFF: lec
deleted: weekly/MGI_MarkerNames.py
Matt Hibbs (Matt.Hibbs@jax.org)
Al Simons (Al.Simons@jax.org)
TAG: reports_db-6-0-25-5
TAG: reports_db-6-0-25-4
TAG: reports_db-6-0-25-3
DATE: 04/28/2025
STAFF: lec
wts2-562/e4g-207/mapping RNA central ids to MGI genes (TR13445)
TAG: reports_db-6-0-25-2
DATE: 03/18/2025
STAFF: lec
wts2-1625/e4g-188/MGI GPI file update/column 8 only
TAG: reports_db-6-0-25-1
DATE: 01/16/2025
STAFF: lec
wts2-1607/e4g-121/Public Reports/NCBI Link Out issue
# modified: ncbilinkout/copy_rpt.csh
mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
TAG: reports_db-6-0-24-15
DATE: 11/19/2024
STAFF: lec
mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
# modified: Configuration.default
TAG: reports_db-6-0-24-14
DATE: 11/06/2024
STAFF: lec
wts2-1577/e4g-65/Update descriptions for MGI_PhenoGenoMP.rpt
TAG: reports_db-6-0-24-13
TAG: reports_db-6-0-24-12
TAG: reports_db-6-0-24-11
TAG: reports_db-6-0-24-10
TAG: reports_db-6-0-24-9
TAG: reports_db-6-0-24-8
TAG: reports_db-6-0-24-7
TAG: reports_db-6-0-24-6
DATE: 10/04/2024, 10/21/2024, 10/28/2024
STAFF: lec
wts2-495/e4g2/e4g-19/Public Report(s) of Comprehensive GXD RNA-Seq Data
new file: gxdrnaseq/GXD_RnaSeq.py
new file: run_gxdrnaseq.csh
modified: Configuration.default
modified: Install
TAG: reports_db-6-0-24-5
DATE: 08/16/2024
STAFF: lec
fl2-948/Create a public report for MGI stat: mouse protein-coding genes with 1-to-1 homology to human
new file: weekly/HOM_ProteinCoding.py
TAG: reports_db-6-0-24-4
TAG: reports_db-6-0-24-3
TAG: reports_db-6-0-24-2
TAG: reports_db-6-0-24-1
DATE: 07/18/2024
STAFF: lec
fl2-898/Trouble getting the MRK_Lists to load
modified: run_weekly.csh
TAG: reports_db-6-0-23-6
DATE: 06/28/2024
STAFF: lec
wts2-1508/fl2-910/User requested change to MRK_List1.rpt
TAG: reports_db-6-0-23-5
DATE: 06/25/2024
STAFF: lec
wts2-1506/fl2-908/Error in MRK_ENSEMBL.rpt
TAG: reports_db-6-0-23-4
DATE: 06/25/2024
STAFF: lec
wts2-1403/index.shtml
TAG: reports_db-6-0-23-3
DATE: 06/06/2024
STAFF: lec
wts2-1489/fl2-895/archive ma2ncit.obo
TAG: reports_db-6-0-23-2
DATE: 04/05/2024
STAFF: lec
wts2-1455/fl2-815/report BIB_PubMed needs to be re-added
# added: weekly/BIB_PubMed.py
# used by Cc: Murphy, Terence (NIH/NLM/NCBI) [E] <murphyte@ncbi.nlm.nih.gov>
#
TAG: reports_db-6-0-23-1
DATE: 03/29/2024
STAFF: lec
# deleted: weekly/BIB_PubMed.py ; no longer used per Stephen Grubb
# deleted: weekly/MGI_GTdbGSS_info.py
# deleted: weekly/MGI_GTDNA.py
# deleted: weekly/MGI_GTGUP.py
# deleted: weekly/MGI_GTRNA.py
# deleted: weekly/GO_terms.py
#
# MGI_GT* reports are *not* removed from FTP site
# deleted: daily/GO_gene_association.py
# mgi.gpad
# gene_association_nonoctua.mgi
# gene_association_nonoctua_pro.mgi
# mgi_nonoctua.gpad
# gene_association.mgi → qcreports_db/mgd/GO_MGIGAF.py
#
TAG: reports_db-6-0-22-8
DATE: 11/04/2023
STAFF: lec
wts2-1314/fl2-617/Add new file to MP files on FTP site
index.shtml
Configuration.default: setenv MPFILES "MPheno_OBO.ontology mp.owl mp.json mp-international.owl"
TAG: reports_db-6-0-22-7
DATE: 10/24/2023
STAFF: sc
https://mgi-jira.atlassian.net/browse/FL2-564
New report: weekly/TAL_MRK_Nomen_Change.py
TAG: reports_db-6-0-22-6
DATE: 06/15/2023
STAFF: sc
wts2-414 - along with this ticket we discovered some production bugs in the HOM reports and in the
index file for the HOM reports that were fixed in this tag
TAG: reports_db-6-0-22-5
TAG: reports_db-6-0-22-4
DATE: 05/12/2023, 05/15/2023
STAFF: lec
wts2-1095/fl2-149/Mouse models of human disease report (1)
wts2-1120/fl2-204/Mouse models of human disease report (2)
weekly/MGI_HumanMouseOneToOne.py
TAG: reports_db-6-0-22-3
TAG: reports_db-6-0-22-2
DATE: 03/24/2023
STAFF: lec
wts2-1137/fl2-247/GOA load scripts update to include GO annotations to 'polymorphic pseudogene'
# modified: daily/GO_gene_association.py
# modified: daily/GO_gpi.py
TAG: reports_db-6-0-22-1
DATE: 02/21/2023
STAFF: lec
wts2-854/fl2-24/Alterations for generating the MGI GPI file.
GO_gpi.py
TAG: reports_db-6-0-21-2
DATE: 07/19/2022
STAFF: lec
wts2-920/Changes to MGI GAF (GO annotations) for consistency of types with those reported in mgi.gpi file
GO_gene_association.py/use SO terms for col 12
TAG: reports_db-6-0-21-1
DATE: 07/18/2022
STAFF: lec
wts2-704/Problem with MGI's latest Europe PMC external links upload
ncbilinkout/pubmed_linkout.py
TAG: reports_db-6-0-20-3
DATE: 06/15/2022
STAFF: sc
added MGIreg.gff3 to index.shtml - apparently this change
dif not get into 6-0-20-1
TAG: reports_db-6-0-20-2
DATE: 06/14/2022
STAFF: lec
wts2-884/Include more granular Sequence Ontology terms for object types in mgi.gpi
TAG: reports_db-6-0-20-1
DATE: 06/06/2022
STAFF: sc
added MGIreg.gff3 to index.shtml
TAG: reports_db-6-0-19-2
TAG: reports_db-6-0-19-1
DATE: 05/20/2022
STAFF: lec
wts2-857/The Rat iso load for GO is adding go_qualifiers during consumption
GO_gene_association.py
TAG: reports_db-6-0-18-5
TAG: reports_db-6-0-18-4
TAG: reports_db-6-0-18-3
TAG: reports_db-6-0-18-2
DATE: 03/23/2022, 03/30/2022, 04/06/2022
STAFF: lec
wts2-703/tr13272/GO-Noctua
GO_gene_association.py
# deleted: weekly/GO_gene_association_nonmouse.py
# rpt_release.csh/remove copy GO_gene_association_nonmouse
# run_daily.csh/add mgi_nonoctua.gpad
# run_daily.csh/add gene_association_nonoctua.mgi
TAG: reports_db-6-0-18-1
DATE: 02/21/2022
STAFF: lec
wts2-767/mgi_notechunk/mgi_note merge
per YAKS, removing obsolete view/report
# deleted: ondemand/MAP_Mapping.py
# deleted: ondemand/MGI_CloneSet.py
# deleted: ondemand_reports.csh
TAG: reports_db-6-0-17-11
TAG: reports_db-6-0-17-10
DATE: 10/19/2021
STAFF: lec
wts2-710/REVERSE/Allow GO annotations to pseudogenes in the public GPAD and GAF files
TAG: reports_db-6-0-17-9
DATE: 10/04/2021
STAFF: lec
wts2-710/Allow GO annotations to pseudogenes in the public GPAD and GAF files
TAG: reports_db-6-0-17-8
DATE: 08/31/2021
STAFF: sc
CHANGES: WTS2-678 Parse Alliance data files by column header, not by position
Alliance clustered and direct preprocessor updates
TAG: reports_db-6-0-17-7
DATE: 08/17/2021
STAFF: sc
MGI_Cov_Human_Gene.py - YAKS-193, update for input file format change
TAG: reports_db-6-0-17-6
DATE: 06/10/2021
STAFF: sc
remove extraneous '>' from index page
TAG: reports_db-6-0-17-5
DATE: 06/10/2021
STAFF: lec
wts2-641/Allow additional go_property (is_active_in) to be valid in Noctua load and reexamine how we define duplicate annotations
GO_gene_association.py
TAG: reports_db-6-0-17-4
TAG: reports_db-6-0-17-3
DATE: 06/09/2021
STAFF: sc
merge tr13349 branch to master - was not done prior to release
Merge output my notes with dates for master and branch:
Updating 0851bca..f38d587
Fast-forward
HISTORY | 10 +++- OK
daily/GO_gpi.py | 20 +++++-- master: 4/7 branch: 4/8
daily/MGI_Cov_Human_Gene.py | 6 +-- master: 5/6 branch: 5/11
index.shtml | 24 ++++----- OK
runone_postgres_report.csh | 63 ---------------------- OK - deleted see b elow
...HGNC_homologene.py => HGNC_AllianceHomology.py} | 41 ++++---------- OK
weekly/HMD_HumanPhenotype.py | 53 ++---------------- master:10/30/20 branch: 3/4
weekly/HOM_AllOrganism.py | 44 ++++++++------- master: 4/2/20 branch: 4/19
weekly/HOM_MouseHumanSequence.py | 35 ++++++------ master: 4/2/20 branch: 4/19
weekly/MGI_DO.py | 27 ++-------- master: 4/2/20 branch: 3/4
weekly/MGI_MarkerNames.py | 8 ++- master: 4/2/20 branch: 2/22
weekly/MGI_iphone_app.py | 17 +++--- master: 4/2/20 branch: 2/22
12 files changed, 116 insertions(+), 232 deletions(-)
delete mode 100755 runone_postgres_report.csh OK
rename weekly/{HGNC_homologene.py => HGNC_AllianceHomology.py} (87%) OK
mode change 100755 => 100644 weekly/MGI_iphone_app.py
TAG: reports_db-6-0-17-2
DATE: 06/07/2021
STAFF: sc
index.shtml - update to GRCm39
DATE: 05/11/2021
STAFF:
TAG: reports_db-6-0-17-1
DATE: 05/11/2021
STAFF: lec
TR13349/Genome Build 39
TAG: reports_db-6-0-16-22
DATE: 05/06/2021
STAFF: lec
CHANGES:
wts2-605/COV reports showing only headers
reports must run as daily reports so they use the production database : bib_workflow_tag must not be empty
TAG: reports_db-6-0-16-21
DATE: 04/27/2021
STAFF: lec
CHANGES:
wts2-606/Human gene COV report has mouse genes
Configuration.default
setenv ALLIANCE_HUMAN_FILE_GZ "/data/downloads/fms.alliancegenome.org/download/DISEASE-ALLIANCE_HUMAN.tsv.gz"
setenv ALLIANCE_HUMAN_FILE "/data/downloads/fms.alliancegenome.org/download/DISEASE-ALLIANCE_HUMAN.tsv"
TAG: reports_db-6-0-16-20
DATE: 04/26/2021
STAFF: lec
CHANGES:
wts2-603/Remove private alleles and strains from the reports for the Coronavirus tables
weekly/MGI_Cov_Allele.py
weekly/MGI_Cov_Strain.py
TAG: reports_db-6-0-16-19
DATE: 04/15/2021
STAFF: lec
CHANGES:
WTS586/Incorrect Evidence Code in MGI GPAD files (TR13494)
daily/GO_gene_association.py
TAG: reports_db-6-0-16-18
DATE: 04/07/2021
STAFF: lec
CHANGES:
TR13491/Add Sanity Check for Withdrawn Markers to MGI/GPI
daily/GO_GPI.py
TAG: reports_db-6-0-16-17
DATE: 04/06/2021
STAFF: sc
CHANGES: Configuration change to static url for input file
TR13459/Coronavirus Reports for Jax Web Resources
MGI_Cov_Human_Gene.py
TAG: reports_db-6-0-16-16
DATE: 04/05/2021
STAFF: lec
CHANGES:
TR13487/Fix header on non-mouse annotation file
TAG: reports_db-6-0-16-15
DATE: 03/11/2021
STAFF: lec
CHANGES:
TR13459/Coronavirus Reports for Jax Web Resources
MGI_Cov_Human_Gene.py
TAG: reports_db-6-0-16-14
DATE: 03/02/2021
STAFF: lec
CHANGES:
TR13272/GO meeting/CalTech/tasks to-do
GO_gene_association.py
TAG: reports_db-6-0-16-13
TAG: reports_db-6-0-16-12
TAG: reports_db-6-0-16-11
TAG: reports_db-6-0-16-10
TAG: reports_db-6-0-16-9
TAG: reports_db-6-0-16-8
TAG: reports_db-6-0-16-7
TAG: reports_db-6-0-16-6
DATE: 02/19/2021
STAFF: lec, sc
CHANGES:
1) update to use Alliance Homology
# HGNC_homologene.py
# HOM_AllOrganism.py
# HOM_MouseHumanSequence.py
# MGI_DO.py
# MGI_MarkerNames.py
# MGI_iphone_app.py
# MGD_HumandPhenotype.py
TR13459/Coronavirus Reports for Jax Web Resources
GAF 2.2
MGI_Cov_Human_Gene.py
MGI_Cov_Mouse_Gene.py
MGI_Cov_Allele.py
MGI_Cov_Strain.py
TR13272/GO meeting/CalTech/tasks to-do
GO_gene_association.py
GO_gpi.py
GO_gene_association_nonmouse.py
TAG: reports_db-6-0-16-5
DATE: 10/30/2020
STAFF: sc
CHANGES: HMD_HumanPhenotype.py
TR13418 - Missing fields in HMD_HumanPhenotyp.rpt
TAG: reports_db-6-0-16-4
DATE: 09/08/2020
STAFF: dbm
CHANGES: MGI_EntrezGene.py - fixed syntax error
TAG: reports_db-6-0-16-3
TAG: reports_db-6-0-16-2
DATE: 08/25/2020
STAFF: lec
TR13272/GPAD 2.0
TAG: reports_db-6-0-16-1
DATE: 08/21/2020
STAFF: lec
TR13204/Infrastructure Release
TAG: reports_db-6-0-15-10
DATE: 08/19/2020
STAFF: lec
TR13359/Europe's PMC link service error
TAG: reports_db-6-0-15-9
TAG: reports_db-6-0-15-8
DATE: 07/31/2020
STAFF: drs
TR13342 - added a link to the Alliance downloads page
TAG: reports_db-6-0-15-7
TAG: reports_db-6-0-15-6
DATE: 07/07/2020
STAFF: sc
TR13082 - added missing configuration for E PMC
TAG: reports_db-6-0-15-6
DATE: 07/06/2020
STAFF: sc
TR13082 bug fix - PMC configuration missing
TAG: reports_db-6-0-15-5
TAG: reports_db-6-0-15-4
DATE: 03/13/2020
STAFF: lec
TR13270/GO meeting/add orcid/daily/GO_gene_association.py
backout change : TR13270/GO meeting/add orcid/daily/GO_gene_association.py
TAG: reports_db-6-0-15-3
TAG: reports_db-6-0-15-2
TAG: reports_db-6-0-15-1
DATE: 03/03/2020
STAFF: sc
TR13229,
1) update Configuration.default MPFILES add mp.json
2) index.shtml - update pheno #1 description and add link
to mp.json
TAG: reports_db-6-0-14-5
DATE: 10/02/2019
STAFF: sc
TR13082 - change description for pmc_providerinfo.xml (note:NCBI/PubMed does
not use the description field.)
TAG: reports_db-6-0-14-4
DATE: 09/25/2019
STAFF: sc
TR13082 - provide NCBI linkout files to E PMC, includes
adding PMC providerinfo.xml
TAG: reports_db-6-0-14-3
DATE: 08/22/2019
STAFF: lec
TR13155/daily/GO_gene_association.py/fix doGPADFinish()
TAG: reports_db-6-0-14-2
DATE: 07/16/2019
STAFF: lec
doGPADFinish/try/except added
TAG: reports_db-6-0-14-1
DATE: 04/03/2019
STAFF: lec
TR12963/teleuse-to-mgd_java_api
TAG: reports_db-6-0-13-7
DATE: 03/28/2019
STAFF: lec
CHANGES: TR13037/HMD_HumanPhenotype.py/use rollup rules for MP
TAG: reports_db-6-0-13-6
DATE: 03/25/2019
STAFF: sc
CHANGES: TR13040 - index.shtml - fix link to gff3 file, remove link to spec.
TAG: reports_db-6-0-13-5
DATE: 03/05/2019
STAFF: lec
CHANGES: TR13049/GO_gene_association.py/use same assignedBy logic for both GAF and GPAD
TAG: reports_db-6-0-13-4
DATE: 01/22/2019
STAFF: lec
CHANGES: TR13010/GO_gene_association.py/addGPADReportRow/add special processing if inferredFrom=InterPro
TAG: reports_db-6-0-13-3
TAG: reports_db-6-0-13-2
DATE: 10/19/2018
STAFF: sc
CHANGES: TR12115 IMPC Crispr allele load
1) new report: weekly/ALL_IMPC_EM.py
TAG: reports_db-6-0-13-1
DATE: 09/04/2018
STAFF: lec
CHANGES: TR12734/GenFevah/Mouse Genome Project
TAG: reports_db-6-0-12-15
DATE: 08/29/2018
STAFF: lec
CHANGES: TR12943
Add weekly/MP_EMAPA.py
TAG: reports_db-6-0-12-14
DATE: 08/10/2018
STAFF: sc
CHANGES: TR12909
Add marker name field to MGI_PhenotypicAllele.rpt
TAG: reports_db-6-0-12-13
DATE: 08/09/2018
STAFF: dbm
CHANGES: set file permissions in the Install script
TAG: reports_db-6-0-12-12
DATE: 08/08/2018
STAFF: sc
CHANGES: bug fix MGI_GenePheno.py, If no MP ID, missing TAB. Extra tab after markers
TAG: reports_db-6-0-12-11
DATE: 08/07/2018
STAFF: lec
CHANGES: TR12910/daily/GO_gene_association.py
change order of qualfier (col 3)
TAG: reports_db-6-0-12-10
DATE: 05/16/2018
STAFF: sc
CHANGES: TR12898 - dupes in seq_marker_cache. These are GT seqeunce tags
that should not be associated with a marker so we set the preferred
accid bit to 0, exclude these from MGI_GTRNA.rpt
TAG: reports_db-6-0-12-9
DATE: 05/16/2018
STAFF: lec
CHANGES: TR12868/noctua cleanup
# modified: daily/GO_gene_association.py
TAG: reports_db-6-0-12-8
DATE: 05/15/2018
STAFF: sc
CHANGES: TR12811
Add reference column to pub Pheno report
14.Genotypes with Sex-specific Phenotypes
TAG: reports_db-6-0-12-7
DATE: 05/11/2018
STAFF: lec
CHANGES: TR12834/GO/Noctua
GO_gene_association.py
TAG: reports_db-6-0-12-6
DATE: 05/10/2018
STAFF: sc
CHANGES:
backed out these changes: TR12867/weekly/MP_EMAPA.py
report and index entry is in TR directory
TAG: reports_db-6-0-12-5
TAG: reports_db-6-0-12-4
DATE: 05/09/2018
STAFF: sc
CHANGES:
TR12867/weekly/MP_EMAPA.py
TAG: reports_db-6-0-12-3
DATE: 04/06/2018
STAFF: lec
CHANGES:
TR12834/daily/GO_gene_association.py
TAG: reports_db-6-0-12-2
TAG: reports_db-6-0-12-1
DATE: 03/07/2018, 03/23/2018
STAFF: lec
CHANGES:
TR12662/GMC/removing obsolete note/sequenceNum
weekly/MGI_iphone_app.py
weekly/VOC_MammalianPhenotype.py
weekly/MGI_Recombinase_Full.py
mgimarkerfeed/mgiMarkerFeed.py
TAG: reports_db-6-0-11-7
DATE: 03/06/2018
STAFF: dbm
CHANGES: TR12805
1) weekly/ES_CellLine.py: Added strain MGI ID
TAG: reports_db-6-0-11-6
DATE: 02/28/2018
STAFF: lec
CHANGES: TR12785//GO_gene_association.py/skip if DAG = 0 (obsolete)
TAG: reports_db-6-0-11-5
DATE: 02/21/2018
STAFF: lec
CHANGES: TR12768//GO_gene_association.py/
GAF/col 15, GPAD/col 10 : UniProt, MGI
TAG: reports_db-6-0-11-4
TAG: reports_db-6-0-11-3
DATE: 11/01/2017
STAFF: sc
CHANGES: TR12566 new phenotypes report with sex-specificity
TAG: reports_db-6-0-11-2
DATE: 10/31/2017
STAFF: lec
CHANGES:
TR12664/daily/GO_gene_associations.py/noctua-model-id
TAG: reports_db-6-0-11-1
DATE: 10/04/2017
STAFF: lec
CHANGES:
TR12250/Lit Triage
1) mgimarkerfeed/new reference type
TAG: reports_db-6-0-10-8
DATE: 07/18/2017
STAFF: dbm
CHANGES:
1) rpt_release_wrapper.csh: removed
2) ncbilinkout/copy_rpt_wrapper.csh; removed
TAG: reports_db-6-0-10-7
DATE: 07/06/2017
STAFF: lec
CHANGES:
TR12615/exclude obsolete MP terms HMD_HumanPhenotype.py
TR12593/exclude obsolete MP terms MGI_PhenotypicAllele.py
TAG: reports_db-6-0-10-3
DATE: 06/14/2017
STAFF: sc
CHANGES: index.shtml - add HGNC Association? column header to HMD_HumanPhenotype.rpt
TAG: reports_db-6-0-10-6
DATE: 06/13/2017
STAFF: sc
CHANGES: TR12613 - MGI_GenePheno.rpt - add missing TAB btwn 3rd and 4th column.
TAG: reports_db-6-0-10-5
DATE: 06/13/2017
STAFF: sc
CHANGES: index.shtml addede HGNC Assoc? column header for HMD_HumanPhenotype.rpt
TAG: reports_db-6-0-10-4
TAG: reports_db-6-0-10-3
DATE: 06/05/2017
STAFF: lec
weekly/MGI_DO.py
remove complicated sorting/replace with simple sorting
TAG: reports_db-6-0-10-2
TAG: reports_db-6-0-10-1
DATE: 04/27/2017, 05/08/2017
STAFF: lec
TR12540/DO (Disease Ontology)
weekly/MGI_DO.py
weekly/MGI_GenePheno.py
weekly/MGI_iphone_app.py
mgimarkerfeed_reports.py
obsolete: weekly/MGI_GeneOMIM.py
HOM* : OMIM ids are for human genes, no change
TAG: reports_db-6-0-8-4
DATE: 03/09/2017
STAFF: lec
CHANGES:
mgimarkerfeed/exclude "reserved" symbols
TAG: reports_db-6-0-8-3
DATE: 3/3/2017
STAFF: dbm
CHANGES:
1) weekly/MGI_IMSRKomp.py: restored the python invocation on line 1 that
somehow got lost
TAG: reports_db-6-0-8-2
DATE: 2/23/2017
STAFF: dbm
CHANGES:
1) run_daily.csh: Copy zipped and unzipped files to ftp directory and make
sure the pairs of files have the same timestamp. The mgi.gpi
report is needed for the GO_GOI_verify QC report, so it can
not be removed from the public report output directory.
TAG: reports_db-6-0-8-1
DATE: 11/02/2016, 02/14/2017
STAFF: lec
CHANGES:
TR12427/Disase Ontology (DO)
TR12502/GO_gene_association.py/synonyms pipe needed
mgimarkerfeed/mgiMarkerFeed.py
MGI_GeneOMIM.py : generates both OMIM & DO file
MGI_GenePhenoDO.py/MGI_Geno_DiseaseDO
MGI_GenePhenoDO.py/MGI_Geno_NotDiseaseDO
mgi_DO.py
obsolete : db.setAutoTranslate
TAG: reports_db-6-0-7-3
DATE: 02/08/2017
STAFF: lec
CHANGES:
1) TR12502/GO_gene_association.py/synonym needs pipe
TAG: reports_db-6-0-7-2
DATE: 1/4/2017
STAFF: dbm
CHANGES:
1) Configuration.default: changed IMSR_STRAINS_CSV to use bhmgiimsr01
TAG: reports_db-6-0-7-1
DATE: 12/20/2016
STAFF: dbm
CHANGES: TR12485
1) run_daily.csh: Remove non-zipped files after creating zipped versions
TAG: reports_db-6-0-6-9
DATE: 11/15/2016
STAFF: sc
CHANGES: TR12404
1) modified HMD_HumanPhenotype.py
TAG: reports_db-6-0-6-8
DATE: 10/31/2016
STAFF: lec
CHANGES:
TR12434/Change NCBI LinkOut PubMed XML
# modified: Configuration.default
# modified: ncbilinkout/nucleotide_linkout.py
# modified: ncbilinkout/protein_linkout.py
# modified: ncbilinkout/pubmed_linkout.py
TAG: reports_db-6-0-6-7
DATE: ?
STAFF: petefrost
CHANGES:
??
TAG: reports_db-6-0-6-6
DATE: 10/10/2016
STAFF: lec
CHANGES:
GO_gene_association.py
TAG: reports_db-6-0-6-5
DATE: 10/06/2016
STAFF: lec
CHANGES:
Install/synmlink/index.shtml
TAG: reports_db-6-0-6-4
DATE: 10/03/2016
STAFF: lec
CHANGES:
mgimarkerfeed/mgimarkerfeed_reports.csh/copy gzip file to FTPREPORTDIR
TAG: reports_db-6-0-6-3
DATE: 09/19/2016
STAFF: dbm
CHANGES: Split the report copying process because the NCBI linkout reports
need to be copied from bhmgidb03lp (where ftp is installed) and all
other reports need to be copied from bhmgiapp01 where sym links to
files under /data/loads exist
1) public_rpt_release.csh: Remove
2) rpt_release.csh: New
3) rpt_release_wrapper.csh: New
4) copy_rpt_2ncbi.csh: Remove
5) copy_rpt.csh: New
6) copy_rpt_wrapper.csh: New
TAG: reports_db-6-0-6-2
TAG: reports_db-6-0-6-1
DATE: 09/08/2016
STAFF: lec
CHANGES:
TR12349/gone-dor & more
TR12345/GPAD/GPI
1) daily/GO_gene_association
2) daily/GO_gpi.py
_Marker_Status_key in (1,3) changed to = 1
ncbilinkout/nucleotide_linkout.py
weekly/GO_gp2protein.py
weekly/HGNC_homologene.py
weekly/MGI_EntrezGene.py
weekly/MGI_GTGUP.py
weekly/MGI_Gene_Model_Coord.py
weekly/MGI_MarkerNames.py
weekly/MGI_OMIM.py
weekly/MGI_iphone_app.py
weekly/MRK_GeneTrap.py
weekly/MRK_List.py
weekly/MRK_Reference.py
weekly/MRK_Sequence.py
weekly/MRK_SwissProt_Sequence.py
3) added to index.shtml TR12339 - new report weekly/MGI_Nonstandard_Strain.py
4) Install : changes for ftp url
5) includes : new for ftp url
6) mgiMarkerfeed/mgiMarkerFeed.py
TAG: reports_db-6-0-5-7
DATE: 08/25/2016
STAFF: kstone
CHANGES: changed ftp url
TAG: reports_db-6-0-5-2
DATE: 08/10/2016
STAFF: lnh
CHANGES: TR12401
1) Removed weekly/MGI_AllGenes.py
TAG: reports_db-6-0-5-1
DATE: 08/02/2016
STAFF: lec
CHANGES: TR12383/TR 11968 HGNC report
1) fixed index.htmml.default
TAG: reports_db-6-0-4-17
DATE: 08/2/2016
STAFF: lnh
CHANGES: TR12383 and TR12401
Restored missing report weekly/MGI_AllGenes.py from cvs archived tag reports_db-5-2-1-14
TAG: reports_db-6-0-4-16
DATE: 07/15/2016
STAFF: sc
CHANGES: TR12339 - new report weekly/MGI_Nonstandard_Strain.py
TAG: reports_db-6-0-4-15
TAG: reports_db-6-0-4-14
DATE: 07/14/2016
STAFF: lnh
CHANGES: TR12036
1) ncbilinkout/ncbilinkout.csh: Removed code section that copies reports to NCBI host
2) ncbilinkout/copy_rpt_2ncbi.csh:Added new script to copy reports to NCBI host
3) public_rpt_release.csh: Added a call to copy the linkout reports to NCBI FTP site.
TAG: reports_db-6-0-4-13
DATE: 07/14/2016
STAFF: lnh
CHANGES:
1) weekly/MGI_PhenotypicAllele.py : TR12373 - Remove section of the code
that filtered out gene association display for Transgenes.
TAG: reports_db-6-0-4-12
DATE: 07/14/2016
STAFF: lec
CHANGES:
1) Configuration.default:setenv GOAMGI
TAG: reports_db-tr12349
TAG: reports_db-tr12349-BP
DATE: 07/07/2016
STAFF: lec
CHANGES:
1) branch point tag for TR12349/gone-dor & more
TAG: reports_db-6-0-4-11
DATE: 07/05/2016
STAFF: dbm
CHANGES:
1) ncbilinkout/nucleotide_linkout.py: removed reference to rsID dictionary
TAG: reports_db-6-0-4-10
DATE: 06/23/2016
STAFF: lec
CHANGES:
TR12361
1) ndex.html.default: accidentally removed 'NAME="strains"' instead of 'NAME="nomenclature"'
TAG: reports_db-6-0-4-9
TAG: reports_db-6-0-4-8
TAG: reports_db-6-0-4-7
TAG: reports_db-6-0-4-6
DATE: 06/21/2016
STAFF: lec
CHANGES:
TR12345/GO/GPAD file
1) generateGPAD.csh: obsolete
2) daily/GO_eco_association.py : obsolete
TAG: reports_db-6-0-4-5
DATE: 05/26/2016
STAFF: lec
CHANGES:
1) index.html : remove Nomenclature
the python report was obsoleted in 2015 but