!version: $Revision: 1.79 $
!date: $Date: 2012/08/14 15:24:47 $
!
! PomBase Reference Collection
!

! The PomBase reference collection is a set of abstracts that can be
! cited to support annotations. It is modeled on the GO reference
! collection (see http://www.geneontology.org/cgi-bin/references.cgi
! and http://www.geneontology.org/doc/GO.references)
!
! data fields for this file:
!
!  pb_ref_id: [mandatory; cardinality 1; PB_REF:nnnnnnn]
!  alt_id: [not mandatory; cardinality 0,1,>1; PB_REF:nnnnnnn]
!  title: [mandatory; cardinality 1; free text]
!  authors: [mandatory; cardinality 1; free text
!            but check whether GO ever switches to cardinality 1,>1 and one entry per author]
!  year: [mandatory, cardinality 1]
!  external_accession: [not mandatory; cardinality 0,1,>1; DB:id]
!  citation: [not mandatory; cardinality 0,1; use for published refs]
!  abstract: [mandatory; cardinality 1; free text]
!  comment: [not mandatory; cardinality 1; free text]
!  is_obsolete: [not mandatory; cardinality 0,1; 'true';
!            if tag is not present, assume that the ref is not obsolete
!            denotes a reference no longer used by the contributing database]
!
!  If another reference collection (e.g. another model organism
!  database) has a record that is equivalent to a PB_REF entry, the
!  database's internal ID should be included as an external_accession
!  for the corresponding PB_REF.
!
! This data is available as a web page at
! *** [URL to fill in] ***
!
pb_ref_id: PB_REF:0000001
title: Protein modification annotation by manual transfer of experimentally-verified annotation data to orthologs based on curator judgment of sequence features.
authors: PomBase curators
year: 2015
abstract: Method for transferring PSI-MOD protein modification annotations to a protein-coding gene based on a curator's judgment of its similarity to a putative ortholog that has annotations that are supported by experimental evidence. Annotations are created when a curator judges that the protein sequence contains a match to a sequence region or motif that is known to be a consensus site for the modification, and when an ortholog has been identified and experimentally determined to have the modification.

pb_ref_id: PB_REF:0000002
title: Manual Ortholog Curation
authors: PomBase curators
year: 2018
abstract: PomBase derives manually curated orthologs from a variety of sources. In some cases the consensus ortholog from the major ortholog predictors (Compara, Inparanoid, OrthoMCL) is used. Many distant orthologs have also been identified by PSI-BLAST matches that are uniformly one-to one across species (described in detail in reference [1]); these alignments have been submitted to the Pfam protein family database. Other ortholog predictions come from experimental data demonstrating functional correspondence or involving membership of corresponding complexes. These predictions are also aligned and submitted to Pfam before inclusion. PomBase's approach ensures that the breadth of coverage is greater than any individual prediction method, and includes many ortholog calls which are not detected by any automated method. Gradually, we will add and display supporting references for all orthology calls. [1] V. Wood (2006), Schizosaccharomyces pombe comparative genomics; from sequence to systems. In: Comparative Genomics Using Fungi as Models (P. Sunnerhagen and J. Piskur, eds.), Topics in Current Genetics 15:233-285.

pb_ref_id: PB_REF:0000003
title: Disease Association Curation
authors: PomBase curators
year: 2018
abstract: PomBase curators manually curate "disease association" annotations for S. pombe genes that have human orthologs, where the ortholog is implicated in disease. Disease descriptions are manually mapped to Monarch Disease Ontology (MONDO) terms via MONDO IDs.

pb_ref_id: PB_REF:0000004
title: Allele Synonyms
authors: PomBase curators
year: 2021
abstract: PomBase curators record synonyms for alleles encountered in the literature, personal communications, or other resources.

pb_ref_id: PB_REF:0000005
title: Allele Comments
authors: PomBase curators
year: 2021
abstract: PomBase curators record comments relevant to alleles, but not suitable for inclusion in allele names or descriptions, encountered in the literature, personal communications, or other resources.