# refs

id: GO_REF:0000028
data:
  {"abstract":"This GO reference describes the criteria used in assigning the evidence codes of IDA (ECO:0000314), IEP (ECO:0000270), ISS (ECO:0000250), IGC (ECO_0000317), RCA (ECO:0000245) and IEA (ECO:0000501) to annotate gene products from PAMGO_MGG. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to iteratively search reciprocal best hits and thus identify orthologs between predicted proteins of Magnaporthe grisea and GO proteins from multiple organisms with published association to GO terms. The alignments were manually reviewed for those hits with e-value equal to zero and with 80% or better coverage of both query and subject sequences, and for those hits with e<=10^-20, pid >=35 and sequence coverage >=80%. Furthermore, experimental or reviewed data from literature and other sources were incorporated into the GO annotation. IDA was assigned to an annotation if normal function of its gene was determined through transfections into a cell line and overexpression. IEP was assigned to an annotation if according to microarray experiments, its gene was upregulated in a biological process and the fold change was equal to or bigger than 10, or if according to Massively Parallel Signature Sequencing (MPSS), its gene was upregulated only in a certain biological process and the fold change was equal to or bigger than 10. ISS was assigned to an annotation if the entry at the With_column was experimentally characterized and the pairwise alignments were manually reviewed. IGC was assigned to an annotation if it based on comparison and analysis of gene location and structure, clustering of genes, and phylogenetic reconstruction of these genes. RCA was assigned to an annotation if it based on integrated computational analysis of whole genome microarray data, and matches to InterPro, pfam, and COG etc. IEA was assigned to an annotation if its function assignment based on computational work, and no manual review was done.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PAMGO_MGG curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG","uniquename":"GO_REF:0000028"}


id: PMID:11921097
data:
  {"abstract":"The dimorphic fission yeast Schizosaccharomyces japonicus has proved to be an excellent experimental model for the investigation of the eukaryotic cell. Here we show that it has a haplontic life cycle, in which the diploid phase is confined to the zygote. To make it amenable to genetic and molecular analysis, we generated genetic markers and cloned a genomic sequence which acts as ars when integrated into a plasmid. Diploids suitable for testing complementation and recombination between markers can be formed by protoplast fusion. The complementation tests and the recombination frequencies determined in octads of spores identified 28 non-allelic groups (genes) of mutations of the auxotrophic and mycelium-negative mutants. Two groups of linked markers were also identified. The cloned fragment, which expresses ars activity, encodes a putative amino acid sequence highly similar to a conserved domain of proteins Cut1 (Schizosaccharomyces pombe), BimB (Aspergillus nidulans) and Esp1 (Saccharomyces cerevisiae).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bozsik A, Szilagyi Z, Benko Z, Sipiczki M","authors_abbrev":"Bozsik A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2002 Apr;19(6):485-98","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2002","pubmed_entrez_date":"2002-03-29","pubmed_publication_date":"Apr 2002","terms_by_termid":{},"title":"Marker construction and cloning of a cut1-like sequence with ARS activity in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:11921097"}


id: GO_REF:0000107
data:
  {"abstract":"GO terms from a source species are projected onto one or more target species based on gene orthology obtained from Ensembl Compara. One-to-one, one-to-many and many-to-many orthology relations and anntations are transferred between orthologs that have at least a 40% peptide identity to each other. Only GO annotations with evidence codes ECO:0000314 (IDA), ECO:0000270 (IEP), ECO:0000316 (IGI), ECO:0000315 (IMP), and ECO:0000353 (IPI), or their descendants, are transferred; annotations with a 'NOT' qualifier are not transferred, and neither are annotations to GO:0005515 (protein binding). Annotations that are transferred using this method receive the evidence code ECO:0000265 (sequence orthology evidence used in automatic assertion), which maps up to the GO Inferred from Electronic Annotation (IEA) evidence code.  The model organism database identifier of the annotation source will be indicated in the 'With' column of the GOA association file.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[85094,99596],"is_not":false,"summary":null,"term":"GO:0044208"},{"annotations":[83717,93741,94089,94740,96873,99896,100852,101258,103476,113772,113870],"is_not":false,"summary":null,"term":"GO:0051083"},{"annotations":[84023],"is_not":false,"summary":null,"term":"GO:0044210"},{"annotations":[93983,95733,99597,106434,106545,110675,113494,115097],"is_not":false,"summary":null,"term":"GO:0006189"},{"annotations":[106689,107270],"is_not":false,"summary":null,"term":"GO:0071266"},{"annotations":[85512,91795,92514],"is_not":false,"summary":null,"term":"GO:0006458"},{"annotations":[89004],"is_not":false,"summary":null,"term":"GO:0036001"},{"annotations":[84024,89597,94673,102686,107257,108095,111730,112881],"is_not":false,"summary":null,"term":"GO:0006207"},{"annotations":[85660,89598,94674,108096,112882],"is_not":false,"summary":null,"term":"GO:0044205"},{"annotations":[86798,90393,98625,112711],"is_not":false,"summary":null,"term":"GO:0006078"},{"annotations":[104526,108594],"is_not":false,"summary":null,"term":"GO:0009257"},{"annotations":[114430],"is_not":false,"summary":null,"term":"GO:0061158"},{"annotations":[86402,96253,114431],"is_not":false,"summary":null,"term":"GO:0070935"},{"annotations":[110949],"is_not":false,"summary":null,"term":"GO:0006666"},{"annotations":[89510,91429,96781,101930],"is_not":false,"summary":null,"term":"GO:0051072"},{"annotations":[93889,106107,111121],"is_not":false,"summary":null,"term":"GO:0006015"},{"annotations":[105319],"is_not":false,"summary":null,"term":"GO:0042791"},{"annotations":[92220],"is_not":false,"summary":null,"term":"GO:0036261"},{"annotations":[95149,103876,104402,112911],"is_not":false,"summary":null,"term":"GO:0006370"},{"annotations":[85132,89135,89366,94440,95407,97776,99282,103053,105873,106063,110058],"is_not":false,"summary":null,"term":"GO:0044571"},{"annotations":[84452,88963,95102,97777,105432,106050,110902,113985],"is_not":false,"summary":null,"term":"GO:0044572"},{"annotations":[97029],"is_not":false,"summary":null,"term":"GO:0019413"},{"annotations":[87621,110516],"is_not":false,"summary":null,"term":"GO:0006083"},{"annotations":[89431,94555],"is_not":false,"summary":null,"term":"GO:0006085"},{"annotations":[112261],"is_not":false,"summary":null,"term":"GO:0019427"},{"annotations":[113200],"is_not":false,"summary":null,"term":"GO:1990181"},{"annotations":[83657,91181,95198,104776,110411,114581],"is_not":false,"summary":null,"term":"GO:0006086"},{"annotations":[87622,94218,110517,111916],"is_not":false,"summary":null,"term":"GO:0006084"},{"annotations":[102874],"is_not":false,"summary":null,"term":"GO:0035348"},{"annotations":[84382,86033,86877,90972,94094,95845,96020,99239,99430,99486,101326,103333,106875,107202,107846,108348,108371,111046,114619,114972],"is_not":false,"summary":null,"term":"GO:0000147"},{"annotations":[97884,99431,101308,103063,103334,104923,108050,108485],"is_not":false,"summary":null,"term":"GO:0051666"},{"annotations":[84486,91465,93899,95004,95065,101309,101327],"is_not":false,"summary":null,"term":"GO:0044396"},{"annotations":[85537],"is_not":false,"summary":null,"term":"GO:0051764"},{"annotations":[84487,89834,90028,91549,93384,95484,95697,98288,98682,100894,102577,103217,104924,108051,111047,113277,114759],"is_not":false,"summary":null,"term":"GO:0030036"},{"annotations":[94095],"is_not":false,"summary":null,"term":"GO:0090135"},{"annotations":[85538,88506,90008,97885,101310,114760],"is_not":false,"summary":null,"term":"GO:0051017"},{"annotations":[95812,104313,112344,114761],"is_not":false,"summary":null,"term":"GO:0061572"},{"annotations":[112345],"is_not":false,"summary":null,"term":"GO:0061573"},{"annotations":[87072],"is_not":false,"summary":null,"term":"GO:0071846"},{"annotations":[88721,97087],"is_not":false,"summary":null,"term":"GO:0030042"},{"annotations":[101311],"is_not":false,"summary":null,"term":"GO:0051639"},{"annotations":[101738],"is_not":false,"summary":null,"term":"GO:0007015"},{"annotations":[88507,90009,93900,95005],"is_not":false,"summary":null,"term":"GO:0030041"},{"annotations":[88722,97088],"is_not":false,"summary":null,"term":"GO:0051014"},{"annotations":[85579],"is_not":false,"summary":null,"term":"GO:0045010"},{"annotations":[86071,90754,92027],"is_not":false,"summary":null,"term":"GO:0051519"},{"annotations":[104147],"is_not":false,"summary":null,"term":"GO:0010846"},{"annotations":[106984],"is_not":false,"summary":null,"term":"GO:0000915"},{"annotations":[85539,94209,94465,104314],"is_not":false,"summary":null,"term":"GO:0071520"},{"annotations":[101312,106985],"is_not":false,"summary":null,"term":"GO:0044837"},{"annotations":[92996,104895],"is_not":false,"summary":null,"term":"GO:0006637"},{"annotations":[96831,106435,106546,113495],"is_not":false,"summary":null,"term":"GO:0046084"},{"annotations":[108726],"is_not":false,"summary":null,"term":"GO:0098702"},{"annotations":[93984],"is_not":fals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