!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. pb_ref_id: PB_REF:0000006 title: Disease associations from Monarch via human-pombe orthologs authors: PomBase curators year: 2024 abstract: Disease associations are created by taking human gene-disease causal and correlated associations created by Monarch (https://monarchinitiative.org) using the MONDO disease ontology (https://mondo.monarchinitiative.org/) and mapping to fission yeast orthologs (https://www.pombase.org/data/orthologs) using the manually maintained fission yeast/human ortholog table. pb_ref_id: PB_REF:0000007 title: Prediction of GPI-anchored proteins with pointer neural networks authors: Magnús Halldór Gíslason, Henrik Nielsen, José Juan Almagro Armenteros, Alexander Rosenberg Johansen. year: 2024 abstract: GPI-anchors constitute a very important post-translational modification, linking many proteins to the outer face of the plasma membrane in eukaryotic cells. Since experimental validation of GPI-anchoring signals is slow and costly, computatinal approaches for predicting them from amino acid sequences are needed. However, the most recent GPI predictor is more than a decade old and considerable progress has been made in machine learning since then. We present a new dataset and a novel method, NetGPI, for GPI signal prediction. NetGPI is based on recurrent neural networks, incorporating an attention mechanism that simultaneously detects GPI-anchoring signals and points out the location of their ω-sites. The performance of NetGPI is superior to existing methods with regards to discrimination between GPI-anchored proteins and other secretory proteins and approximate (±1 position) placement of the ω-site. comment: Prediction tool available at this URL https://services.healthtech.dtu.dk/services/NetGPI-1.1/. pb_ref_id: PB_REF:0000008 title: Distant orthologs supported by Pfam-N authors: PomBase curators year: 2024 abstract: Ortholog predicted using Pfam-N (PMID: 35190689), and manually reviewed and manually reviewed for context (length, functional attributes and other features). See DOI: 10.1007/4735_97 for a description of our manual review process. pb_ref_id: PB_REF:0000009 title: Distant orthologs supported by JackHMMR authors: PomBase curators year: 2024 abstract: Ortholog predicted using jackHMMER iterative search (PMID:25943547), and manually reviewed for context (length, functional attributes and other features). See DOI: 10.1007/4735_97 for a description of our manual review process.