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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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| − | ==Location of project-related files on Textpresso==
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| − | http://textpresso-dev.caltech.edu/concise_descriptions/
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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. Gene regulation data <br \>
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| − | 9. Molecular Function <br \>
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| − | 10. Tissue expression (may include life-stage) <br \>
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| − | 11. 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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| − | Phenotypes
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| − | <Gene> mutants exhibit the following phenotypes, <phenotypes>.
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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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| − | *Source 1: GO data in postgres
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| − | **Paper -- gop_paper
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| − | **WBGene -- gop_wbgene
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| − | **GO -- gop_goontology
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| − | **GO Term -- gop_goid
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| − | *Source 2: GO file from Protein2GO called gp_association.ace
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| − | **
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| − | *Source 3: gene_association file
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| − | **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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| − | *Source 4: Topic data
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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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| − | *Source 1: Phenotype OA, PG table name:(Phenotypes are added to variation and not genes)
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| − | *Source 2: Acedb tag: Under ?Gene, Reference_allele ?Variation and Allele ?Variation and Under ?Variation Phenotype
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| − | *Source 3: 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 1: gene_association.wb
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| − | **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 'IGI' in column 7 indicate a physical interaction between the WBgenes in column 2/3 and column 8
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| − | **Rows with a 'IPI" in column 7 indicate a genetic interaction between the WBgenes in column 2/3 and column 8
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| − | *Source 2: 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. Gene regulation data
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| − | *Caltech data
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| − | *Source: Gene regulation data in genereg OA
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| − | **Positive_regulate Anatomy_term "<grg_pos_anatomy>"
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| − | **Positive_regulate Life_stage "<grg_pos_lifestage>"
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| − | **Positive_regulate Subcellular_localization "<grg_pos_scl>"
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| − | **Positive_regulate Subcellular_localization_text "<grg_pos_scltext>"
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| − | **Negative_regulate Anatomy_term "<grg_neg_anatomy>"
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| − | **Negative_regulate Life_stage "<grg_neg_lifestage>"
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| − | **Negative_regulate Subcellular_localization "<grg_neg_scl>"
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| − | **Negative_regulate Subcellular_localization_text "<grg_neg_scltext>"
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| − | **Does_not_regulate Anatomy_term "<grg_not_anatomy>"
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| − | **Does_not_regulate Life_stage "<grg_not_lifestage>"
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| − | **Does_not_regulate Subcellular_localization "<grg_subcellloc>"
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| − | **Does_not_regulate Subcellular_localization_text "<grg_not_scltext>"
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| − | **Trans_regulated_gene "<grg_transregulated>"
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| − | **Trans_regulator_gene "<grg_transregulator>"
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| − | **No Subdata Result "<grg_result>"
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| − | 9. Molecular Function
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| − | *Caltech data: GO Molecular Function
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| − | *Source 1: GO OA, PG table name:
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| − | *Source 3: gene_association.WSXXX.c_elegans file:
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| − | **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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| − | 10. Tissue expression and life stage
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| − | *Caltech data
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| − | *Source 1: Expression data
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| − | *OA (exprpat), PG table names:
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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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| − | 11. Sub-cellular localization
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| − | *Caltech data
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| − | *Source 1: GO cellular component
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| − | *Source 2: gene_association file
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| − | **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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