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fix broken/legacy identifiers.org URLs #126

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Schmoho opened this issue Jul 19, 2024 · 0 comments
Open

fix broken/legacy identifiers.org URLs #126

Schmoho opened this issue Jul 19, 2024 · 0 comments
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2.2 feature Issues that aim to introduce new feature in ModelPolisher.

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@Schmoho
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Schmoho commented Jul 19, 2024

I just went through Biomodels, BiGG and some models of our group to find identifiers.org URLs that are not using valid namespaces.

Labeled as "feature" because this aims to repair broken data, not annotate and curate valid data.

Here is the list of those where it is obvious how to repair them:

 ["reactome.compound"  "http://identifiers.org/reactome.compound/8851513"]
 ["reactome.reaction"  "http://identifiers.org/reactome.reaction/R-SCE-70523"]
 ["biomodels.sbo" "http://identifiers.org/biomodels.sbo/SBO:0000281"]
 ["inchi_key" "http://identifiers.org/inchi_key/BGWGXPAPYGQALX-OEXCPVAWSA-L"]
 ["ncbigi" "http://identifiers.org/ncbigi/16129989"]
 ["obo.bto" "http://identifiers.org/obo.bto/BTO:0000575"]
 ["obo.chebi" "http://identifiers.org/obo.chebi/CHEBI:33704"]
 ["obo.fma" "http://identifiers.org/obo.fma/FMA:74531"]
 ["obo.go" "http://identifiers.org/obo.go/GO:0004674"]
 ["obo.pato" "http://identifiers.org/obo.pato/PATO:0001021"]
 ["obo.psi-mod" "http://identifiers.org/obo.psi-mod/MOD:00890"]
 ["obo.pw" "http://identifiers.org/obo.pw/PW:0000565"]
 ["psi-mod" "http://identifiers.org/psi-mod/MOD:00000"]
 ["psimod" "http://identifiers.org/psimod/MOD:00048"]
 ["seed.reactions" "https://identifiers.org/seed.reactions:rxn01396"]

For those I have no clue:

 ["bind" "http://identifiers.org/bind/50058"]
 ["EnsemblGenomes-Gn"  "http://identifiers.org/EnsemblGenomes-Gn/ECUMN_4058"]
 ["EnsemblGenomes-Tr"  "http://identifiers.org/EnsemblGenomes-Tr/CAP75598"]
 ["omim" "http://identifiers.org/omim/601417"]
 ["PSEUDO" "http://identifiers.org/PSEUDO/CAB14182.3"]
 ["psimi" "http://identifiers.org/psimi/MI:0501"]
 ["refseq_locus_tag"  "http://identifiers.org/refseq_locus_tag/EC55989_0350"]
 ["refseq_name" "http://identifiers.org/refseq_name/cls-1"]
 ["refseq_old_locus_tag"  "http://identifiers.org/refseq_old_locus_tag/S_0338"]
 ["refseq_orf_id" "http://identifiers.org/refseq_orf_id/sll1027"]
 ["refseq_synonym" "http://identifiers.org/refseq_synonym/CTE-II"]
 ["sabiork" "http://identifiers.org/sabiork/9859"]
 ["unit" "https://identifiers.org/unit/UO:0000040"]
 ["unknown" "http://identifiers.org/unknown/10.1074/jbc.C000664200"]
@Schmoho Schmoho added the feature Issues that aim to introduce new feature in ModelPolisher. label Jul 19, 2024
@Schmoho Schmoho changed the title Scraping for invalid identifiers.org URLs fix broken/legacy identifiers.org URLs Sep 17, 2024
@Schmoho Schmoho added the 2.2 label Sep 17, 2024
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