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Adding documentation/provenance
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@cmungall
cmungall committed Jul 9, 2020
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45 changes: 35 additions & 10 deletions curated/ORFs/uniprot_sars-cov-2.gpi
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!gpi-version: 1.2
!
!This file contains additional information for proteins in the UniProt KnowledgeBase (UniProtKB).
!Protein accessions are represented in this file even if there is no associated GO annotation.
! This file contains information about the proteome of SARS-CoV-2, in GPI format
!
! The file is based on information provided by UniProt, but includes additional curated information
!
! The following sources were used:
!
! - UniProtKB GPI file (ftp://ftp.ebi.ac.uk/pub/contrib/goa/uniprot_sars-cov-2.gpi)
! - SciBite CORD-19 Vocabulary (https://github.com/SciBiteLabs/CORD19)
! - The Protein Ontology (https://proconsortium.org/download/development/pro_sars2.gpi)
! - Additional knowledge about protein nomenclature acquired as part of National Lab funded SARS-CoV-2 efforts (NVBL and LDRD)
!
! Some key properties:
! - we include an entry for each functional protein, including non-structural proteins cleaved from polypeptides
! - we use chain IDs of the form UniProtKB:P0DTC1-PRO_0000449645 for NSPs
! - we do *not* include all chain IDs; in particular:
! - we only use when necessary, for NSPs
! - NSP1-10 have duplicate entries in UniProt, there are two polyprotein entries with identical sequence prior to frameshift
! - we use the longer pp parent as the canonical/reference entry. This decision is synced with what IntAct uses
!
! It is intended to be used for different purpose:
!
! - The canonical set of annotatable function-capable entities used by the Gene Ontology project
! - Use in Knowledge Graphs, such as https://github.com/Knowledge-Graph-Hub/kg-covid-19/
! - Vocabulary for Natural Language Processing / Concept Recognition
!
! The file is maintained in GitHub in this repo: https://github.com/Knowledge-Graph-Hub/kg-covid-19/
!
! More information on the original provenance of this file can be found at: https://github.com/geneontology/go-site/issues/1431
!
!Columns:
!
! name required? cardinality GAF column # Example content
! DB required 1 1 UniProtKB
! DB_Object_ID required 1 2/17 Q4VCS5-1
! DB_Object_Symbol required 1 3 AMOT
! DB_Object_Name optional 0 or greater 10 Angiomotin
! DB_Object_Synonym(s) optional 0 or greater 11 AMOT|KIAA1071
! DB_Object_ID required 1 2/17 P0DTC1, P0DTC1-PRO_0000449645
! DB_Object_Symbol required 1 3 nsp11
! DB_Object_Name optional 0 or greater 10 Non-structural protein 11
! DB_Object_Synonym(s) optional 0 or greater 11 PL-PRO
! DB_Object_Type required 1 12 protein
! Taxon required 1 13 taxon:9606
! Taxon required 1 13 taxon:2697049
! Parent_Object_ID optional 0 or 1 - UniProtKB:Q4VCS5
! DB_Xref(s) optional 0 or greater - WB:WBGene00000035
! Properties optional 0 or greater - "db_subset=Swiss-Prot|target_set=KRUK,BHFL"
! DB_Xref(s) optional 0 or greater - PR:000050270
! Properties optional 0 or greater - not used yet
!
!Generated: 2020-06-10 13:25
!
UniProtKB P0DTC1 pp1a Replicase polyprotein 1a ORF1a|1a|pp1a|ORF1a/ClvPrd (SARS2)|ORF1a proteolytic cleavage product protein taxon:2697049 PR:P0DTC1-1
UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 P0DTC1(4393-4405)|rep/Clv:nsp11 (SARS2)|UniProtKB:P0DTC1, 4393-4405|nsp11 (SARS2)|PRO_0000449645|Non-structural protein 11|nsp-11|nsp11|ns11|ns-11|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 11 protein taxon:2697049 UniProtKB:P0DTC1 PR:000050280
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