Textpresso-based automated extraction of concise descriptions

Generating gene sets with and without concise descriptions

Set of genes with a concise description

Query for all genes with a concise description from Postgres: Relevant postgres table names:

• con_wbgene: Stores the WBGene ID and gene names
• con_desctype: Type of description (relevant for us: Concise_description)
• con_desctext: Text of the concise description

Query for all WBGenes that have a concise description (in con_desctext AND con_desctype):

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;

• Number of genes with a concise description (as of 05.07.2014)=6,624

Location of project-related files on Textpresso

http://textpresso-dev.caltech.edu/concise_descriptions/

Semantic categories in a Concise Description

1. Molecular identity
2. Orthology/Similarity
3. Mutant Phenotypes
4. Processes
5. Pathways
6. Genetic Interaction
7. Physical Interaction
8. Molecular Function
9. Tissue expression (may include life-stage)
10. Sub-cellular localization (may include life-stage)

Template for a Concise Description

Molecular identity
<Gene> encodes .....;
Orthology/Similarity
<Gene> is (orthologous, similar) to .....;
Phenotypes
<Gene> mutants exhibit the following phenotypes, <phenotypes>.
Process/Pathway
<Gene> is (required, functions, regulates, is involved in, is part of) ....., as mutants of <gene> exhibit <phenotypes>;
Genetic interaction with respect to Process or Pathway
<Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>;
Physical interaction
<Protein> physically interacts with (protein, DNA, RNA) .....;
Molecular Function
<Protein> has ..... activity in (in vitro, in vivo) assays;
Tissue Expression
<Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) 
regulated by <Gene/Protein>.....;
Sub-cellular localization 
<Protein> is localized to <cellular component> and expression in <cellular component> 
is <positively, negatively> regulated by .....

Note: Not all descriptions may follow the exact order or choice of words.

Data mining (mining data from Postgres and/or Acedb) for the semantic categories

1. Molecular identity and Orthology data (Homology, Orthology and Paralog data)

• Non-caltech data, curated at Hinxton
• Ace tags: ?Gene Ortholog_other, Paralog
• Contact: Michael Paulini

3. Processes

• Caltech data
• 2 sources: GO data and Topic data
• Sources for GO data: GO OA and GO file from Protein2GO
  • GO OA, Postgres (PG) table name:
• Easier to use the gene_association file:ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
  • File name:gene_association.WS243.wb.c_elegans
  • Rows with a 'P' in column 9 indicates GO Biological Process associated with a gene.
• Contact Person: Kimberly, Ranjana

• Topic OA:
  • OA field:Gene, PG table name:pro_wbgene
  • OA field:WBPaper, PG table name:pro_paper
• Contact Person: Karen

4. Pathway (No database source for now?)

5. Mutant Phenotypes

• Caltech data
• Phenotype OA, PG table name:(Phenotypes are added to variation and not genes)
• Acedb tag: Under ?Gene, Reference_allele ?Variation and Allele ?Variation and Under ?Variation Phenotype
• Might be easier to use the phenotype_association file:ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
  • File name:phenotype_association.WS243.wb
• Contact Person: Karen

6. Genetic Interaction and 7. Physical Interaction

• Caltech data
• Source: Interaction OA and tables
  • "Field Name" = Postgres Table:
  • "Paper" = int_paper
  • "Interaction Type" = int_type
  • "Bait overlapping gene" = int_genebait
  • "Target overlapping gene" = int_genetarget
  • "Non-directional Gene(s)" = int_genenondir
  • "Effector Gene(s)" = int_geneone
  • "Affected Gene(s)" = int_genetwo

Example statements:

If int_type = "Physical"

<int_genebait> interacts physically with <int_genetarget> (and vice versa)

If int_type = "Genetic - Synthetic ( Synthetic )"

<int_genenondir> interacts with <other int_genenondir(s)> in a synthetic genetic interaction

If int_type = "Genetic - Suppression ( Suppression )"

<int_geneone> genetically suppresses <int_genetwo>

8. Molecular Function

• Caltech data: GO Molecular Function
• File for GO data (for protein-encoding genes only):
• GO OA, PG table name:
• Might be easier to use the gene_association.WSXXX.c_elegans file:
  • ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
  • Rows with a 'F' in column 9 indicates GO molecular function associated with a gene.
• Contact Person: Kimberly, Ranjana

9. Tissue expression and life stage

• Caltech data
• Expression OA (exprpat), PG table names:
  • exp_anatomy for anatomy terms
  • exp_goid for subcell localization
  • exp_lifestage for life stage
  • exp_paper for paper
  • exp_gene for gene
• Contact Person: Daniela

10. Sub-cellular localization

• Caltech data
• Source: GO cellular component
• Source 1: gene_association file
  • ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
  • File name:gene_association.WS243.wb.c_elegans

Publications related to Text-mining methods

• Automatically generating gene summaries from biomedical literature.

Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B.

Pac Symp Biocomput. 2006:40-51.

PMID:17094226

• Generating gene summaries from biomedical literature: A study of semi-structured summarization

Xu Ling *, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz

Information Processing and Management 43 (2007) 1777–1791

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