Difference between revisions of "Textpresso-based automated extraction of concise descriptions"

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'''Process'''
 
'''Process'''
*Rule 1: If a gene has terms with both IEA and non-IEA evidence codes, use only the non-IEA terms.
+
*Rule 1: Ignore all IEA and ISS process terms
 
*Rule 2: Exclusions:
 
*Rule 2: Exclusions:
 
**Ignore the term 'reproduction'[IMP]
 
**Ignore the term 'reproduction'[IMP]
 
**Ignore the term 'embryo development ending in birth or egg hatching[IMP]'
 
**Ignore the term 'embryo development ending in birth or egg hatching[IMP]'
 +
*Rule 3: If a GO term has the words 'involved in' anywhere, beginning, middle or at the end, use the words 'functions in'
 +
**Data: WBGene00006495,cpna-1,striated muscle contraction involved in embryonic body morphogenesis[IMP],WB_REF:WBPaper00041875|PMID:23283987
 +
**Sentence: cpna-1 functions in striated muscle contraction involved in embryonic body morphogenesis;
 +
*Rule 4: For the GO term 'synaptic transmission, <word>' switch the order of words to make it '<word> synaptic transmission'.
 +
*Example for Rule 4:
 +
**WBGene00011488,nra-2, synaptic transmission, cholinergic[IMP],WB_REF:WBPaper00034730|PMID:19609303,,WB,locomotion[IMP],protein processing[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR008710,regulation of signal transduction[IEA],INTERPRO:IPR016574
 +
**nra-2 is involved in cholinergic synaptic transmission and locomotion.
  
 +
*Rule 5: For all other Process terms the sentence will be:
 +
**<Gene> is involved in <process term>;
 +
**Examples:
 +
**WBGene00014123,elpc-3,tRNA wobble uridine modification[IMP],WB_REF:WBPaper00034713|PMID:19593383,,WB,translation[IMP],spermatogenesis[IGI],olfactory learning[IMP],vulval development[IGI],embryonic morphogenesis[IGI],oocyte development[IGI]
 +
**Sentence: elpc-3 is involved in tRNA wobble uridine modification, translation, spermatogenesis, olfactory learning, vulval development and embryonic morphogenesis.
  
Data: WBGene00006495,cpna-1,striated muscle contraction involved in embryonic body morphogenesis[IMP],WB_REF:WBPaper00041875|PMID:23283987
+
*Rule 6: For the term 'molting cycle, collagen and cuticulin-based cuticle' GO term, drop the comma and the words 'collagen and cuticulin-based cuticle'
<Gene> is involved in <process term>;
+
**Example:
*Sentence: cpna-1 is involved in striated muscle contraction involved in embryonic body morphogenesis.
+
**WBGene00016643,vps-45,molting cycle, collagen and cuticulin-based cuticle[IMP],WB_REF:WBPaper00029049|PMID:17235359,,WB,vesicle docking involved in exocytosis[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR001619,vesicle-mediated transport[IEA]
 
+
**Sentence: vps-45 is involved in '''the''' molting cycle;
 
 
  
 
'''Molecular identity'''
 
'''Molecular identity'''

Revision as of 21:45, 16 June 2014

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

Set of genes with no concise description

Set of genes with no concise description and at least one published paper

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. Gene regulation data
9. Molecular Function
10. Tissue expression (may include life-stage)
11. Sub-cellular localization (may include life-stage)

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

1. Molecular identity

  • Caltech and non-caltech data?
  • Source 1: GO data
    • Download gene_association.wb.gz for C.elegans from GO consortium: http://www.geneontology.org/GO.current.annotations.shtml?all
    • All rows with column 15 (assigned by) with 'WB' are WormBase annotations, those with 'UniProtKB' or 'InterPro' are from those databases
    • Need data from these rows:
      • where column 9 has value 'F' (Molecular Function)
      • column 2, associated genes, has UniProt ID or WormBase GeneID, need to translate UniProtID to WormBase ID.
      • column 3: DB_Object symbol, eg, wht-7,
      • column 5: GOID, eg, GO:0000346
      • column 6: DB:Reference (Reference), eg.PMID:12062106, GO_REF:0000002
      • column 7: Evidence code, eg, IMP
      • column 15: Assigned By, eg., WB (which database created the annotation)
    • For translation of UniProt IDs to WormBase Gene Ids use the file gp2protein.wb.gz at http://www.geneontology.org/gp2protein/
  • Source 2: Homology data, see #2

2. Orthology, Homology and Paralog data

  • Ace tags: ?Gene Ortholog_other, Paralog
  • Contact: Michael Paulini

3. Processes

  • Caltech data
  • GO data
  • Source 1: Download gene_association.wb.gz for C. elegans from GO consortium: http://www.geneontology.org/GO.current.annotations.shtml?all
    • All rows with column 15 (assigned by) with 'WB' are WormBase annotations, those with 'UniProtKB' or 'InterPro' are from those databases
    • Need data from these rows:
      • where column 9: has value 'P' (Process),
      • column 2 (DB_Object ID): the associated genes, UniProt ID or WBGene ID,
      • column 3 (DB_Object symbol), eg, wht-7, GO terms are from column 5.
      • column 5: GOID, eg, GO:0000346
      • column 6: DB:Reference (Reference), eg.PMID:12062106, GO_REF:0000002
      • column 7: Evidence code, eg, IMP
      • column 8: With, eg. 'WB:WBRNAi00000785|WBPhenotype:0000050'
  • GO data in postgres
    • Paper -- gop_paper
    • WBGene -- gop_wbgene
    • GO -- gop_goontology
    • GO Term -- gop_goid
  • Contact Person: Kimberly, Ranjana
  • Source 2: Topic data
    • 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
  • Source 1: Phenotype OA, PG table name:(Phenotypes are added to variation and not genes)
  • Source 2: Acedb tag: Under ?Gene, Reference_allele ?Variation and Allele ?Variation and Under ?Variation Phenotype
  • Source 3: phenotype_association file:ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
    • File name:phenotype_association.WS243.wb
    • Following rows:
      • Rows with 'NOT' should be ignored for this search.
      • column 2, associated genes, WormBase GeneID
      • column 3: DB_Object symbol, eg, aap-1,
      • column 5: Phenotype ID, eg, WBPhenotype:0000674
      • column 6: DB:Reference (Reference), eg.WB_REF:WBPaper00032243, or WB:WBVar00249743
  • Contact Person: Karen

6. Genetic Interaction and 7. Physical Interaction

  • Caltech data
  • Source 1: gene_association.wb
    • ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/ONTOLOGY/
    • File name:gene_association.WS243.wb.c_elegans
    • Rows with a 'IGI' in column 7 indicate a genetic interaction between the WBgenes in column 2/3 and column 8
    • Rows with a 'IPI" in column 7 indicate a physical interaction between the WBgenes in column 2/3 and column 8
  • Source 2: 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. Gene regulation

  • Caltech data
  • Source: Gene regulation data in genereg OA
    • Positive_regulate Anatomy_term "<grg_pos_anatomy>"
    • Positive_regulate Life_stage "<grg_pos_lifestage>"
    • Positive_regulate Subcellular_localization "<grg_pos_scl>"
    • Positive_regulate Subcellular_localization_text "<grg_pos_scltext>"
    • Negative_regulate Anatomy_term "<grg_neg_anatomy>"
    • Negative_regulate Life_stage "<grg_neg_lifestage>"
    • Negative_regulate Subcellular_localization "<grg_neg_scl>"
    • Negative_regulate Subcellular_localization_text "<grg_neg_scltext>"
    • Does_not_regulate Anatomy_term "<grg_not_anatomy>"
    • Does_not_regulate Life_stage "<grg_not_lifestage>"
    • Does_not_regulate Subcellular_localization "<grg_subcellloc>"
    • Does_not_regulate Subcellular_localization_text "<grg_not_scltext>"
    • Trans_regulated_gene "<grg_transregulated>"
    • Trans_regulator_gene "<grg_transregulator>"
    • No Subdata Result "<grg_result>"

9. Molecular Function

  • Caltech data: GO Molecular Function
  • Source 1: Download gene_association.wb.gz for C. elegans from GO consortium: http://www.geneontology.org/GO.current.annotations.shtml?all
    • All rows with column 15 (assigned by) with 'WB' are WormBase annotations, those with 'UniProtKB' or 'InterPro' are from those databases
    • Need data from these rows:
      • where column 9: has value 'F' (Molecular Function),
      • column 2 (DB_Object ID): the associated genes, UniProt ID or WBGene ID,
      • column 3 (DB_Object symbol), eg, wht-7, GO terms are from column 5.
      • column 5: GOID, eg, GO:0000346
      • column 6: DB:Reference (Reference), eg.PMID:12062106, GO_REF:0000002
      • column 7: Evidence code, eg, IDA
  • Contact Person: Kimberly, Ranjana

10. Tissue expression and life stage

  • Caltech data
  • Source 1: Expression data
  • 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

11. Sub-cellular localization

  • Caltech data
  • GO data
  • Source 1: gene_association file for C. elegans at:http://www.geneontology.org/GO.current.annotations.shtml?all
    • Need data from these rows:
      • where column 9 has value 'C' (Cellular Component)
      • column 2, associated genes, has UniProt ID or WormBase GeneID, need to translate UniProtID to WormBase ID.
      • column 3: DB_Object symbol, eg, wht-7,
      • column 5: GOID, eg, GO:0000346
      • column 7: Evidence code, eg, IDA

Rule 1:

Template for a Concise Description

For the test phase, order of sentences:

  • Orthology
  • Process
  • Component
  • Function/identity


Orthology/Similarity
<Gene> is (orthologous, similar) to <human gene>;
Phenotypes
<Gene> mutants exhibit the following phenotypes: <phenotypes>.
Process/Pathway
<Gene> is (required, functions, regulates, is involved in, is part of) <process>;
Genetic interaction with respect to Process or Pathway
<Gene> interacts genetically with <gene1, gene2>;
Physical interaction
<Protein> physically interacts with (protein, DNA, RNA) .....;
Molecular Function
<Protein> has <molecular function>..... activity in (in vitro, in vivo);
Tissue Expression and sub-cellular localization
<Gene/Protein> is expressed in <tissue> and localized to <GO cellular component>;

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

Rules for automated sentence construction

Homology

<Gene> encodes a protein orthologous to human <human protein name>;

Process

  • Rule 1: Ignore all IEA and ISS process terms
  • Rule 2: Exclusions:
    • Ignore the term 'reproduction'[IMP]
    • Ignore the term 'embryo development ending in birth or egg hatching[IMP]'
  • Rule 3: If a GO term has the words 'involved in' anywhere, beginning, middle or at the end, use the words 'functions in'
    • Data: WBGene00006495,cpna-1,striated muscle contraction involved in embryonic body morphogenesis[IMP],WB_REF:WBPaper00041875|PMID:23283987
    • Sentence: cpna-1 functions in striated muscle contraction involved in embryonic body morphogenesis;
  • Rule 4: For the GO term 'synaptic transmission, <word>' switch the order of words to make it '<word> synaptic transmission'.
  • Example for Rule 4:
    • WBGene00011488,nra-2, synaptic transmission, cholinergic[IMP],WB_REF:WBPaper00034730|PMID:19609303,,WB,locomotion[IMP],protein processing[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR008710,regulation of signal transduction[IEA],INTERPRO:IPR016574
    • nra-2 is involved in cholinergic synaptic transmission and locomotion.
  • Rule 5: For all other Process terms the sentence will be:
    • <Gene> is involved in <process term>;
    • Examples:
    • WBGene00014123,elpc-3,tRNA wobble uridine modification[IMP],WB_REF:WBPaper00034713|PMID:19593383,,WB,translation[IMP],spermatogenesis[IGI],olfactory learning[IMP],vulval development[IGI],embryonic morphogenesis[IGI],oocyte development[IGI]
    • Sentence: elpc-3 is involved in tRNA wobble uridine modification, translation, spermatogenesis, olfactory learning, vulval development and embryonic morphogenesis.
  • Rule 6: For the term 'molting cycle, collagen and cuticulin-based cuticle' GO term, drop the comma and the words 'collagen and cuticulin-based cuticle'
    • Example:
    • WBGene00016643,vps-45,molting cycle, collagen and cuticulin-based cuticle[IMP],WB_REF:WBPaper00029049|PMID:17235359,,WB,vesicle docking involved in exocytosis[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR001619,vesicle-mediated transport[IEA]
    • Sentence: vps-45 is involved in the molting cycle;

Molecular identity

  • Rule 1: If the evidence code is 'IEA' and 'activity' term is present, add the words 'based on protein domain information' to the sentence:
    • Sentence: <Gene> is predicted to have <activity term>, based on protein domain information.
  • Rule 2: If Evidence code is non-IEA
  • Rule 3: Exclusion list:
    • Ignore the term 'protein binding'
    • Sentence: Gene exhibits <activity term, binding term>, based on experimental evidence.


Component

  • Rule 1: Ignore all IEA and ISS GO terms, use only non-IEA GO terms
    • Sentence: <Gene> is localized to <component term>;
  • Rule 2: For 'integral component of ....' terms add the words 'is an';
    • Eg. for Rule 2: WBGene00006319,sup-10,integral component of plasma membrane[IDA],WB_REF:WBPaper00006135|PMID:14534247,,WB,striated muscle dense body[IDA]
    • sup-10 is an integral component of plasma membrane and is localized to striated muscle dense body;


  • Examples
    • WBGene00023405,sor-1,nucleoplasm[IDA],WB_REF:WBPaper00027128|PMID:16501168,,WB,nuclear speck[IDA]
    • Sentence: sor-1 is localized to the nucleoplasm and nuclear speck;
    • WBGene00004681,rsd-2,nucleolus[IDA],WB_REF:WBPaper00044261|PMID:18430922,,WB,endoplasmic reticulum[IDA],cytosol[IDA]
    • Sentence: rsd-2 is localized to the nucleolus, endoplasmic reticulum and cytosol;
    • WBGene00021827,dnc-6,dynactin complex[IDA],WB_REF:WBPaper00037699|PMID:20964796,,WB
    • Sentence: dnc-6 is localized to the dynactin complex;

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


Back To Concise Descriptions