Incorrect linkout patterns or example identifiers

ariutta commented 9 years ago

The following linkout pattern + example identifier combinations appear to be outdated or incorrect:

Do not resolve:

[x] NuGO wiki: http://wiki.nugo.org/index.php/HMDB00001
[x] LIPID MAPS: http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=LMPR0102010012
[x] Gramene Rice and Rice Ensembl Gene: see bridgedb/datasources#3
[x] UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgTracks?position=uc001tyh.1
[x] RFAM: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00066
[x] IPI: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=IPI00000001&format=default
[x] miRBase Sequence: http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=MI0000001
[x] MatrixDB: http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=P00747_P07355&class=Association
[x] MINT: http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=MINT-10000
[x] Ensembl Dog: http://www.ensembl.org/Canis_familiaris/Gene/Summary?g=ENSCAFG00000025860
[x] Small Molecule Pathway Database: http://pathman.smpdb.ca/pathways/SMP00001/pathway

Outdated:

[x] Pfam: http://pfam.sanger.ac.uk/family/PF01234/ should be http://pfam.xfam.org/family/PF01234/
[x] PharmGKB Pathways: http://www.pharmgkb.org/pathway/PA146123006 should be https://www.pharmgkb.org/pathway/PA146123006
[x] PharmGKB Drug: http://www.pharmgkb.org/drug/PA448710 should be https://www.pharmgkb.org/drug/PA448710
[x] PharmGKB Gene: http://www.pharmgkb.org/gene/PA131 should be https://www.pharmgkb.org/gene/PA131
[x] SGD: http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000028457 should be http://www.yeastgenome.org/locus/S000028457/overview
[x] EcoGene: http://ecogene.org/geneInfo.php?eg_id=EG10173 should be http://www.ecogene.org/old/geneInfo.php?eg_id=EG10173
[x] Gramene Maize: http://www.maizesequence.org/Zea_mays/Gene/Summary?g=GRMZM2G174107 should be http://www.gramene.org/Zea_mays/Gene/Summary?g=GRMZM2G174107 or http://ensembl.gramene.org/Zea_mays/Gene/Summary?g=GRMZM2G174107
[x] Gramene Genes: http://www.gramene.org/db/genes/search_gene?acc=GR:0060184 should be http://archive.gramene.org/db/genes/search_gene?acc=GR:0060184
[x] TAIR Locus: http://arabidopsis.org/servlets/TairObject?type=locus&name=AT1G01030 should be https://www.arabidopsis.org/servlets/TairObject?type=locus&name=AT1G01030
[x] Wikidata: http://www.wikidata.org/wiki/Q407962 should be https://www.wikidata.org/wiki/Q407962
[x] Wikipedia: http://en.wikipedia.org/wiki/Acetate should be https://en.wikipedia.org/wiki/Acetate
[x] Rat Genome Database: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=2018 should be http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=2018
[x] RefSeq: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_012345 should be http://www.ncbi.nlm.nih.gov/protein/NP_012345
[x] MaizeGDB: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=acc1 should be http://maizegdb.org/gene_center/gene/acc1
[x] BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.1.1.1 should be http://www.brenda-enzymes.org/enzyme.php?ecno=1.1.1.1

egonw commented 3 years ago

BRENDA updated: https://github.com/bridgedb/datasources/commit/64d367e8e7a04ea266f9bb29591adeb0606389cd

egonw commented 3 years ago

Updated RefSeq: https://github.com/bridgedb/datasources/commit/451ba059d5abc6502048310517746861615b7e29

egonw commented 3 years ago

egonw commented 4 months ago

Updated a few more and for two complicated ones I filed new issues.

bridgedb / datasources

Incorrect linkout patterns or example identifiers #8