!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: 
year: 
abstract:Sources of manually curated orthologs in PomBase may vary.  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; these alignments have been submitted to the Pfam protein family database. This process is described in detail in Wood V; Schizosaccharomyces pombe comparative genomics; from sequence to systems. In: Comparative
 Genomics using fungi as models (P. Sunnerhagen, J. Piskur, eds.) Topics in Current Genetics vol 15, pp
233- 285 (2006).  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.