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| − | ==Generating gene sets with and without concise descriptions==
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| − | ====Set of genes with a concise description====
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| − | Query for all genes with a concise description from Postgres:
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| − | Relevant postgres table names:
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| − | *con_wbgene: Stores the WBGene ID and gene names
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| − | *con_desctype: Type of description (relevant for us: Concise_description)
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| − | *con_desctext: Text of the concise description
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| − | Query for all WBGenes that have a concise description (in con_desctext AND con_desctype):
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| − | SELECT DISTINCT(con_wbgene) FROM con_wbgene WHERE joinkey IN (SELECT joinkey FROM con_desctext WHERE con_desctext IS NOT NULL) AND joinkey IN (SELECT joinkey FROM con_desctype WHERE con_desctype IS NOT NULL) ORDER BY con_wbgene;
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| − | *Number of genes with a concise description (as of 05.07.2014)=6,624
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| − | ====Set of genes with no concise description====
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| − | ====Set of genes with no concise description and at least one published paper====
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| − | ==Semantic categories in a Concise Description==
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| − | 1. Molecular identity <br \>
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| − | 2. Orthology/Similarity <br \>
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| − | 3. Mutant Phenotypes <br \>
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| − | 4. Processes <br \>
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| − | 5. Pathways <br \>
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| − | 6. Genetic Interaction<br \>
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| − | 7. Physical Interaction <br \>
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| − | 8. Molecular Function <br \>
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| − | 9. Tissue expression (may include life-stage) <br \>
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| − | 10. Sub-cellular localization (may include life-stage) <br \>
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| − | ==Template for a Concise Description==
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| − | '''Molecular identity'''
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| − | <Gene> encodes .....;
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| − | '''Orthology/Similarity'''
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| − | <Gene> is (orthologous, similar) to .....;
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| − | '''Process/Pathway'''
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| − | <Gene> is (required, functions, regulates, is involved in, is part of) ....., as mutants of <gene> exhibit <phenotypes>;
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| − | '''Genetic interaction with respect to Process or Pathway'''
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| − | <Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>;
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| − | '''Physical interaction'''
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| − | <Protein> physically interacts with (protein, DNA, RNA) .....;
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| − | '''Molecular Function'''
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| − | <Protein> has ..... activity in (in vitro, in vivo) assays;
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| − | '''Tissue Expression'''
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| − | <Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively)
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| − | regulated by <Gene/Protein>.....;
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| − | '''Sub-cellular localization'''
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| − | <Protein> is localized to <cellular component> and expression in <cellular component>
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| − | is <positively, negatively> regulated by .....
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| − | Note: Not all descriptions may follow the exact order or choice of words.
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| − | ==Data mining (mining data from Postgres and/or Acedb) for the semantic categories==
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| − | 1. Molecular identity and Orthology data (Homology, Orthology and Paralog data)
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| − | *Non-caltech data, curated at Hinxton
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| − | *Ace tags: ?Gene Ortholog_other, Paralog
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| − | *Contact: Michael Paulini
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| − | 3. Processes
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| − | *Caltech data
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| − | *2 sources: GO data and Topic data
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| − | *Sources for GO data: GO OA and GO file from Protein2GO
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| − | *GO OA, Postgres (PG) table name:
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| − | *Easier to use the gene_association file:ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
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| − | *File name:gene_association.WS243.wb.c_elegans
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| − | *Rows with a 'P' in column 9 indicates GO Biological Process associated with a gene.
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| − | *Contact Person: Kimberly, Ranjana
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| − | *Topic OA:
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| − | *OA field:Gene, PG table name:pro_wbgene
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| − | *OA field:WBPaper, PG table name:pro_paper
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| − | *Contact Person: Karen
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| − | 4. Pathway
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| − | (No database source for now?)
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| − | 5. Mutant Phenotypes
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| − | *Caltech data
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| − | *Phenotype OA, PG table name:(Phenotypes are added to variation and not genes)
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| − | *Acedb tag: Under ?Gene, Reference_allele ?Variation and Allele ?Variation and Under ?Variation Phenotype
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| − | *Might be easier to use the phenotype_association file:ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
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| − | *File name:phenotype_association.WS243.wb
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| − | *Contact Person: Karen
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| − | 6. Genetic Interaction and 7. Physical Interaction
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| − | *Caltech data
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| − | *Source: Interaction OA and tables
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| − | *"Field Name" = Postgres Table:
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| − | *"Paper" = int_paper
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| − | *"Interaction Type" = int_type
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| − | *"Bait overlapping gene" = int_genebait
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| − | *"Target overlapping gene" = int_genetarget
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| − | *"Non-directional Gene(s)" = int_genenondir
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| − | *"Effector Gene(s)" = int_geneone
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| − | *"Affected Gene(s)" = int_genetwo
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| − | Example statements:
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| − | If int_type = "Physical"
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| − | <int_genebait> interacts physically with <int_genetarget> (and vice versa)
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| − | If int_type = "Genetic - Synthetic ( Synthetic )"
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| − | <int_genenondir> interacts with <other int_genenondir(s)> in a synthetic
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| − | genetic interaction
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| − | If int_type = "Genetic - Suppression ( Suppression )"
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| − | <int_geneone> genetically suppresses <int_genetwo>
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| − | 8. Molecular Function
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| − | *Caltech data: GO Molecular Function
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| − | *File for GO data (for protein-encoding genes only):
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| − | *GO OA, PG table name:
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| − | *Might be easier to use the gene_association.WSXXX.c_elegans file:Index of ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
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| − | *Rows with a 'F' in column 9 indicates GO molecular function associated with a gene.
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| − | *Contact Person: Kimberly, Ranjana
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| − | 9. Tissue expression and life stage
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| − | *Caltech data
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| − | *Expression OA (exprpat), PG table names:
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| − | *tables are:
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| − | *exp_anatomy for anatomy terms
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| − | *exp_goid for subcell localization
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| − | *exp_lifestage for life stage
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| − | *exp_paper for paper
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| − | *exp_gene for gene
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| − | *Contact Person: Daniela
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| − | 10. Sub-cellular localization
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| − | *Caltech data
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| − | *Source: GO cellular component
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| − | *Source 1-ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
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| − | *File name:gene_association.WS243.wb.c_elegans
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| − | ====Publications related to Text-mining methods====
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| − | *Automatically generating gene summaries from biomedical literature.
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| − | Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B.
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| − | Pac Symp Biocomput. 2006:40-51.
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| − | PMID:17094226
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| − | *Generating gene summaries from biomedical literature: A study of semi-structured summarization
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| − | Xu Ling *, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
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| − | Information Processing and Management 43 (2007) 1777–1791
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| − | Back To [[Concise Descriptions]]
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