Difference between revisions of "Generation of automated descriptions"

From WormBaseWiki
Jump to navigationJump to search
Line 128: Line 128:
  
 
==Process==
 
==Process==
==Template for a process sentence==
+
====Template for a process sentence====
 
<Gene> is (required, functions, regulates, is involved in, is part of) <process>;
 
<Gene> is (required, functions, regulates, is involved in, is part of) <process>;
  
Line 144: Line 144:
 
***column 8: With, eg. 'WB:WBRNAi00000785|WBPhenotype:0000050'
 
***column 8: With, eg. 'WB:WBRNAi00000785|WBPhenotype:0000050'
  
===Rules for process sentence construction====
+
====Rules for process sentence construction====
 
*'''Rule 1''': Ignore all IEA and ISS process terms
 
*'''Rule 1''': Ignore all IEA and ISS process terms
 
*'''Rule 2''': For all IMP terms, add the words 'based on mutant phenotype' at the end of the sentence.
 
*'''Rule 2''': For all IMP terms, add the words 'based on mutant phenotype' at the end of the sentence.

Revision as of 22:00, 20 November 2014

Contents

Querying for gene sets

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/

Location of the manual concise description files:

  • For viewing the latest dump:

http://tazendra.caltech.edu/~postgres/cgi-bin/data/concise_dump_new.ace

  • Script: /home/postgres/work/citace_upload/concise/dump_concise.pl
  • File location: /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace

Semantic categories in an Automated Description

1. Orthology/Similarity/Molecular identity
2. Processes
3. Molecular Function
4. Sub-cellular localiztion
5. Tissue expression (not done yet)

Orthology/Homology

Source files

Going forward we will use the Best BlastP files for C. elegans from the latest release, eg for WS246: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/ 1. Best BlastP hits file: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS246.best_blastp_hits.txt.gz

2. Mapping of elegans genes to proteins: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS246.xrefs.txt.gz

3. Orthologs file: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS246.orthologs.txt.gz

Template of an Orthology sentence

<Gene> encodes an ortholog of <human protein>;

Rules for orthology sentence construction

  • Rule 1: If the words 'family member' occurs in the description between words before it and after it, then ignore 'family member'
    • Examples:
    • 'aldehyde dehydrogenase 8 family member a1’ becomes 'aldehyde dehydrogenase 8a1'
    • 'aldehyde dehydrogenase 9 family member a1' becomes 'aldehyde dehydrogenase 9a1'

Jul 2, 2014:

  • Rule 2: If the words 'human Uncharacterized protein' occur ignore this homology
    • Examples:
    • ctg-1 encodes an ortholog of human Uncharacterized protein;
    • mtp-18 encodes an ortholog of human Uncharacterized protein;
  • Rule 3 : If 2 or more of these words occur: 'family', 'subfamily', group', 'member' 'polypeptide' or 'class', ignore them and resolve as in examples:
    • olfactory receptor, family 56, subfamily B, member 1 becomes olfactory receptor 56B1
    • potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 becomes potassium intermediate/small conductance calcium-activated channel N2
    • potassium inwardly-rectifying channel, subfamily J, member 12 becomes human potassium inwardly-rectifying channel J12
    • nuclear receptor subfamily 3, group C, member 2 becomes nuclear receptor 3C2
    • nuclear receptor subfamily 5, group A, member 2 becomes nuclear receptor 5A2
    • nuclear receptor subfamily 1, group H, member 4 becomes nuclear receptor 1H4
    • cytochrome P450, family 3, subfamily A, polypeptide 5 becomes cytochrome P450 3A5
    • cytochrome P450, family 21, subfamily A, polypeptide 2 becomes cytochrome P450 21A2
    • UDP glycosyltransferase 3 family, polypeptide A1 becomes UDP glycosyltransferase 3A1
    • mannosidase, alpha, class 1B, member 1 becomes human mannosidase, alpha, 1B1
    • phosphatidylinositol glycan anchor biosynthesis, class V stays as is, because the word 'class' occurs by itself.
    • scavenger receptor class B, member 2 becomes scavenger receptor B2
  • Rule 4: If the word 'homolog' co-occurs with a species name = 'Drosophila', 'S. cerevisiae', 'yeast', inside brackets , ignore 'homolog' and move the species without the brackets.
    • salvador homolog 1 (Drosophila) becomes Drosophila and human salvador 1
    • SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) becomes S. cerevisia and human SSU72 RNA polymerase II CTD phosphatase
    • translocase of outer mitochondrial membrane 22 homolog (yeast) becomes yeast and human translocase of outer mitochondrial membrane 22
    • human vacuolar protein sorting 4 homolog B (S. cerevisiae) becomes S. cerevisiae and human vacuolar protein sorting 4
    • unconventional SNARE in the ER 1 homolog (S. cerevisiae) becomes S. cerevisiae and human unconventional SNARE in the ER 1
  • Rule 5: if the description field (meaning human protein name), has '(C.elegans)' in it (these refer to an elegans gene, making it circular), then ignore the description field and use the HGNC symbol instead (accession number lookup to symbol required).
    • Examples:
      • Data: WBGene00017948,mth-1,ENSEMBL:ENSP00000407190,ENSG00000166979,ENST00000435323,eva-1 homolog C (C. elegans) [Source:HGNC Symbol;Acc:13239],EVA1C,EVA1C,EVA1C-005,EVA1C,EVA 1 HOMOLOG C PRECURSOR FAM176C
      • Sentence: mth-1 encodes an ortholog of human EVA1C (HGNC:EVA1C);.
      • Data:WBGene00004895,smu-1,ENSEMBL:ENSP00000380336,ENSG00000122692,ENST00000397149,smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247],SMU1,SMU1,SMU1-001,SMU1,WD40 REPEAT CONTAINING SMU1 SMU 1 SUPPRESSOR OF MEC 8 AND UNC 52 HOMOLOG
      • Sentence: smu-1 encodes an ortholog of human SMU1 (HGNC:SMU1);.
      • Data: WBGene00044079,tag-241,ENSEMBL:ENSP00000287482,ENSG00000156876,ENST00000287482,spindle assembly 6 homolog (C. elegans) [Source:HGNC Symbol;Acc:25403],SASS6,SASS6,SASS6-001,SASS6,SPINDLE ASSEMBLY ABNORMAL 6 HOMOLOG
      • Sentence: tag-241 encodes an ortholog of human SASS6 (HGNC:SASS6);.
  • Rule 6: Ignore the text string '<numeral>kDa at the end of terms and the trailing comma, including within parentheses.
    • cleavage and polyadenylation specific factor 4, 30kDa becomes cleavage and polyadenylation specific factor 4
    • cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa becomes cleavage stimulation factor, 3' pre-RNA, subunit 1
    • nucleoporin 153kDa becomes nucleoporin
  • Rule 7 : Grab the HGNC symbol and the place it on the end of the sentence, within parentheses as ', (HGNC symbol:<HGNC symbol>)'

Explanation of Orthology/homology information in WormBase

1. Orthology, Homology and Paralog data

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

From Michael Paulini:

 
a.) orthology
it is in the ACeDB database on the genes as ortholog/paralog/ortholog_other, but we also dump it since a while each build (as   example, here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/annotation 
/c_elegans.PRJNA13758.WS243.orthologs.txt.gz). 

b.) homology
1. protein homology)
the blastx data is in the GFF files, as well as here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/acedb                 /Non_C_elegans_BLAST
for C.elegans the patch file is also loaded during the build, so you can find them as regular Homology_data on the respective  parent sequences in ACeDB.

the blastp data is as Homology_data on the proteins, as well as partially dumped into that one: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS243.best_blastp_hits.txt.gz

We also go protein clusters (mostly eggNOG based ones), which show homoloy and shared function and are connected to the member proteins in ACeDB through the Homology_group tag .

2. nucleotide homology) 
Mostlyy based on blat, but with the current release switched to star
You can find them in the respective GFF files and also similar to the blastx as homology data on the parent sequences in ACeDB

We also got RNASeq, which currently lives as RNASeq features in the GFF and ACeDB, but also as expression level data in the Gene/Transcript/CDS.

And last, but not least, we got pairwise whole genome alignments for selected species, which currently we only show on EnsEMBL Genomes, but you can use the generic Compara API to pull the alignments from there.

As orthology + homology covers such a huge swath of very different data in WormBase, there is no unifying format, except ACeDB and to a certain extent GFF.


Process

Template for a process sentence

<Gene> is (required, functions, regulates, is involved in, is part of) <process>;

Source file for Process data

  • Source: gene_association file for C.elegans from the WormBase FTP site:
    • ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS243/ONTOLOGY/gene_association.WS243.wb.c_elegans
    • 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'

Rules for process sentence construction

  • Rule 1: Ignore all IEA and ISS process terms
  • Rule 2: For all IMP terms, add the words 'based on mutant phenotype' at the end of the sentence.
    • Examples:
    • Data: WBGene00001972,hmg-1.2,cell fate specification[IMP],WB_REF:WBPaper00003453|PMID:10197987,,WB,gonad development[IMP],Wnt signaling pathway[IGI],vulval development[IMP]
    • Sentence: hmg-1.2 is involved in cell fat=e specification, gonad development and vulval development, based on mutant phenotypes.
    • Data: WBGene00002148,gon-14,muscle contraction[IMP],WB_REF:WBPaper00024213|PMID:15133127,,WB,defecation[IGI],gonad morphogenesis[IMP],multicellular organism growth[IGI],regulation of pharyngeal pumping[IMP]
    • Sentence: gon-14 is involved in muscle contraction, gonad morphogenesis and regulation of pharyngeal pumping, based on mutant phenotypes and in defecation and growth.

Rule 3: No exclusions as of 07.07.2014, leave in reproduction:

  • Rule 4 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 5: For all other Process terms the sentence will be:
    • <Gene> is involved in <process term>;
    • Examples:
    • Data: 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:
    • Data: 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;
  • Rule 7: Replacement rule:
    • Replace term 'multicellular organism growth' with 'growth'.
    • Replace term 'embryo development ending in birth or egg hatching' with 'embryo development'
    • Replace term 'synaptic transmission, <word>' with '<word> synaptic transmission'.
      • Example Data: 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
      • Sentence: nra-2 is involved in cholinergic synaptic transmission and locomotion.

Rule 8: Granularity rule:

  • If a GO term in the list is a parent of (is_a or part_of parent) another GO term in the list, keep the most granular child term and ignore the parent terms.

Molecular function/identity

Source file for molecular function data

  • Caltech and non-caltech data?
  • Source 1: GO data
    • Download the gene_association file for C.elegans from the WormBase FTP site:
    • ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS243/ONTOLOGY/gene_association.WS243.wb.c_elegans
    • 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 8: 'With (or) From' eg., INTERPRO:IPR002293,
      • column 15: Assigned By, eg., WB (which database created the annotation)

Rules for molecular function sentence construction

  • Rule 1: Exclusion list:
    • Ignore the term 'protein binding'
    • Ignore the term 'binding'
  • Rule 2: Order the IDA and IMP terms first in the sentence followed by ISS and IEA terms.
  • Rule 3: If the evidence code is 'IEA' and 'activity' term is present, add the words 'predicted to have <activity term>' and add the words ', based on protein domain information' to the sentence:
    • Sentence: <Gene> is predicted to have <activity term>, based on protein domain information.
  • Examples:
    • WBGene00000108,alh-2,oxidoreductase activity[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR015590,WB,oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor[IEA],INTERPRO:IPR016163
    • alh-2 is predicted to have oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, based on protein domain information.
  • Rule 3: If Evidence code is 'ISS' add the words 'based on sequence information' to the sentence
    • WBGene00001951,hlh-4,sequence-specific DNA binding transcription factor activity[ISS],WB_REF:WBPaper00034761|PMID:19632181,,WB,protein dimerization activity[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR011598,DNA binding[IEA],INTERPRO:IPR015660
    • Sentence: hlh-4 is predicted to have sequence-specific DNA binding transcription factor activity based on sequence information, protein dimerization activity and DNA binding activity, based on protein domain information.
  • Rule 4: If a binding term is present add the word 'activity' to it.
  • Rule 5: If the evidence code is IDA, IMP, IGI, IPI, or IEP add the words 'exhibits' before the GO term and 'based on experimental evidence' after the GO term and/or at the end of the sentence.
    • IDA example:
    • WBGene00001952,hlh-6,RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity[IDA],WB_REF:WBPaper00032277|PMID:18927627,,WB,protein dimerization activity[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR011598,DNA binding[IEA],INTERPRO:IPR015660
    • Sentence: hlh-6 exhibits RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity and is predicted to have protein dimerization activity and DNA binding activity.
    • IMP example:
    • WBGene00009583,aagr-3,alpha-glucosidase activity[IMP],WB_REF:WBPaper00036069|PMID:20349118,,WB,hydrolase activity, hydrolyzing O-glycosyl compounds[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR000322,catalytic activity[IEA],INTERPRO:IPR011013,carbohydrate binding[IEA]
    • Sentence: aagr-3 exhibits alpha-glucosidase activity and is predicted to have hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity, and carbohydrate binding activity, based on protein domain information.

Rule 6: For non-IEA terms beginning with 'structural constituent of <word>', use the words 'is a 'structural constituent of <word>' in the sentence.

  • Example:
    • WBGene00010783,mrpl-36,structural constituent of ribosome[IEA],PMID:12520011|PMID:12654719,INTERPRO:IPR000473,WB
    • Sentence: mrpl-36 is a structural constituent of ribosome, based on protein domain information.
    • WBGene00010783,mrpl-36,structural constituent of ribosome[ISS]
    • Sentence: mrpl-36 is a structural constituent of ribosome, based on sequence information.
    • WBGene00010783,mrpl-36,structural constituent of ribosome[IMP] or [IDA]
    • Sentence: mrpl-36 is a structural constituent of ribosome.
  • Rule 7 Replacement
    • For GO term: 'oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor' becomes 'oxidoreductase activity, acting on the aldehyde or oxo group of donors' (drop the text string 'NAD or NADP as acceptor')
  • Rule 8: If a GO term has a comma in it, then add a comma after this GO term and the next ‘and’.
  • Rule 9: Always put the GO terms with experimental evidence codes (EXP, IMP, IGI, IPI, IDA, IEP) first in the sentence, followed by the Automatic and Computational Analysis Evidence Codes (IEA, ISS, ISA, ISO, ISM, IGC, IBA, IBD, IKR, IRD and RCA).

Sub-cellular localization

Source file for Sub-cellular localization 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



Order of sentences

  • Orthology
  • Process
  • Function/identity
  • Component

Tissue expression

Source files for Tissue expression data

  • Source 1: Expression data
  • OA (exprpat), PG table names:
    • for all these tables where exp_endogenous table value 'endogenous', grab the exp_gene, WBGeneXXXXXXXX
    • exp_name, values look like Expr1005.
    • exp_anatomy for anatomy terms, in the form of Wbt:0003679, translate these IDs using the anatomy ontology file
    • anatomy ontology file from ftp site:ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS244/ONTOLOGY/anatomy_ontology.WS244.obo
    • exp_paper for paper
    • exp_qualifier for the qualifiers 'certain’, ‘uncertain’ and ‘partial’.
  • Contact Person: Daniela


Rules for tissue expression sentence construction

Rule 1: Use only the data that has the qualifiers 'Certain' and 'Partial' and ignore all those data that have 'uncertain'.

Rule 2: Pick an anatomy term only once

  • Sentence: <Gene> is expressed in the <anatomy term1, anatomy term2 and anatomy term3>;
  • Examples:
  • Data for alh-10:
  • WBGene00000116 alh-10 Expr5583 nervous system,intestine,tail neuron WBPaper00031006,WBPaper00006525 Endogenous
  • Sentence: alh-10 is expressed in the nervous system, intestine and tail neuron;


  • Data for asp-5:
  • WBGene00000218 asp-5 Expr5817 intestine WBPaper00031006,WBPaper00006525 Endogenous
  • WBGene00000218 asp-5 Expr4352 intestine WBPaper00028802 Endogenous
  • Sentence: asp-5 is expressed in the intestine;


  • Data for ccr-4:
  • WBGene00000376 ccr-4 Expr4479 pharynx WBPaper00027076 Endogenous
  • WBGene00000376 ccr-4 Expr11132 male,hermaphrodite,somatic cell,germ line *WBPaper00043886 Endogenous
  • WBGene00000376 ccr-4 Expr4479 hyp6,hyp5,hyp4,hyp3,hyp2,hyp1,pharyngeal neuron,head muscle WBPaper00027076 Endogenous
  • WBGene00000376 ccr-4 Expr7174 pharynx,hypodermis,seam cell *WBPaper00031006,WBPaper00006525 Endogenous
  • WBGene00000376 ccr-4 Expr4480 pharynx,body wall musculature,head neuron,tail neuron *WBPaper00027076 Endogenous
  • WBGene00000376 ccr-4 Expr4480 hyp6,hyp5,hyp4,hyp3,hyp2,hyp1,pharyngeal neuron,head muscle
  • Sentence: ccr-4 is expressed in the pharynx, somatic cell, germ line, hyp6, hyp5, hyp4, hyp3, hyp2, hyp1, pharyngeal neuron, head muscle, hypodermis, seam cell, body wall musculature and in the head and tail neurons.
  • Rule 3: Replacement Rule
  • Replacement 1: If the anatomy term 'cell' occurs by itself, then use the words 'widely expressed' instead of 'cell'.
    • sentence: col-178 is expressed in the Cell;
    • Becomes: col-178 is expressed widely.
  • Replacement 2: If the anatomy term 'cell' is present with other anatomy terms, use instead the words 'expressed in several tissues including the' <other anatomy terms>
    • Sentence: frm-1 is expressed in the intestine, pharynx, and the Cell;
    • Becomes: frm-1 is expressed in several tissues including the intestine and pharynx.
  • Replacement 3: If the anatomy term 'neuron' occurs as an anatomy term by itself, use the words 'in the nervous system' instead.
    • Sentence: ceh-82 is expressed in the neuron;
    • Becomes: ceh-82 is expressed in the nervous system;


  • Replacement 4: If the word 'neuron' occurs as part of an anatomy term, eg, 'head neuron', pluralize it, except for the exceptions:
    • Exceptions:
    • I3 neuron
    • I4 neuron
    • I5 neuron
    • I6 neuron
    • M1 neuron
    • M4 neuron
    • M5 neuron
    • MI neuron
    • Sentence: nhr-194 is expressed in the amphid neuron, ciliated neuron, head neuron, and the sensory neuron;
    • Becomes: nhr-194 is expressed in the amphid neurons, ciliated neurons, head neurons, and the sensory neurons;


Rule 5: Granularity Rule: When a string of cell names are present, check to see if any parent terms are present in any ExprXXX for that gene, keep the highest common parent term available.

Rules for sentence construction: Sub-cellular localization/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;

Preliminary results

These descriptions are based on Homology predictions and the GO annotations for Process, Component and Function:

 

*alh-2
alh-2 encodes an ortholog of human dehydrogenase aldehyde dehydrogenase family 1 member dehydrogenase; alh-2 is predicted to have oxidoreductase activity and oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor based on protein domain information.

*asp-5
asp-5 encodes an ortholog of human cathepsin d; asp-5 is involved in cell death and locomotion; asp-5 is predicted to have aspartic-type endopeptidase activity based on protein domain information.

*cng-1
cng-1 encodes an ortholog of human cyclic nucleotide gated channel alpha 3; cng-1 is predicted to have ion channel activity based on protein domain information; cng-1 is localized to the neuronal cell body.

Mapping of automated concise description data to OA fields

Mapping of data to data fields in the OA
OA field
number
OA field name Data to be inserted Example of data
to be inserted
Required or Not OA table name
1 WBGene WBGene WBGene000 Required con_wbgene
2 Curator Name of Curator James Done(first then replace with) Ranjana Kishore
(insert for all rows)
Required con_curator
3 Curator History Name of Curator same as pgid
(insert for all rows)
Required con_curhistory
4 Description Type Automated_concise_description
(insert for all rows)
Automated_concise_description Required con_desctype
5 Description Text the automated concise description asp-19 encodes an ortholog... Required con_desctext
6 Reference WBPaper WBPaper00026979 Required con_paper
7 Accesssion Evidence For Homology use ENSEMBL ID
For Process, Function, use InterPro ID
ENSEMBL:ENSP00000431595
INTERPRO:IPR002293
(comma separate multiple values)
Not required con_accession
8 Last Updated Date when the descriptions
were last generated
2014-09-11 Required con_lastupdate
9 pgid pgid 1149
(Postgres will generate)
Required

Tab-delimited file for OA insert

  • Order of the data will be: WBGene, Date, Paper, Accession_evidence, Automated_concise_description, Inferred_automatically text
  • Format: tab-delimited file, comma separate the values when multiple values are present
  • Date is the last date that the script was run to generate the automated descriptions (eg. 2014-05-28)
  • File will be placed on textpresso-dev to be picked up by a cron job by JC

Inserting automated descriptions into the OA/postgres

The automated descritpions belong to a new 'Description Type' added to the OA, as dropdown, and in WBGene Term Info

The script to populate is here : /home/postgres/work/pgpopulation/concise_description/20140909_automated_concise/populate_automated_concise_descriptions.pl

Always gets data from : http://textpresso-dev.caltech.edu/concise_descriptions/semantic_categories/concise_descriptions/OA_concise_descriptions.txt

When populating for each OA row that has con_desctype set to 'Automated_concise_description', it will delete from these tables :

  • con_wbgene
  • con_curator
  • con_curhistory
  • con_desctext
  • con_paper
  • con_accession
  • con_lastupdate

Meaning that it's keeping the 'Automated_concise_description' value, so that future runs of the script will reuse existing pgids. When running out of pre-existing pgids, it will create a new one and assign 'Automated_concise_description' to con_desctype

Dumping the automated descriptions

Location of script for populating Tazendra postgres

/home/postgres/work/pgpopulation/concise_description/20140909_automated_concise/populate_automated_concise_descriptions.pl

Location of scripts

  • Run the dumping script manually, on tazendra: /home/acedb/kimberly/citace_upload/concise/wrapper.pl
  • The file, concise_dump_new.ace, can be scp-ed for testing from:scp acedb@tazendra.caltech.edu:/home/postgres/public_html/cgi-bin/data/concise_dump_new.ace

For now we will not do the following:


  • Concise descriptions dumper at /home/postgres/work/citace_upload/concise/dump_concise.pl
  • /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace

Text for Automatically_inferred tag

Tag looks like: Evidence Automatically_inferred ?Text

Text will be: This description was automatically generated by Textpresso scripts based on homology/orthology data and Gene Ontology (GO) annotations from the WS243 version of WormBase.

.ace format

List of tags to be dumped:

  • Automated_description
  • Paper_evidence
  • Accession_evidence
  • Date_last_updated
  • Inferred_automatically: Do we add a field to the OA, will be a free text field? or should this happen at the dumper level, where the release number will change everytime, and text might change as well; prefer a field in the OA.
Gene : "WBGene00009585"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Date_last_updated	"2012-07-24"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Paper_evidence	"WBPaper000045688"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Paper_evidence	"WBPaper000045689"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Acession_evidence "ENSEMBL" "ENSP00000419081"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Acession_evidence "INTERPRO" "IPR002048"
Automated_description	"cal-7 encodes an ortholog of human calmodulin-like 4 (HGNC:CALML4); cal-7 is predicted to have calcium ion binding activity, based on protein domain information."	Inferred_automatically "This description was generated automatically by Textpresso scripts based on homology/orthology data and Gene Ontology (GO) annotations, from the WS243 version of WormBase."	

Numbers from citace testing

  • concise_dump_new.ace was scped from: /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace and tested
  • Tested concise_dump_new.ace on empty citaceminus mirrror on local machine with the WS246 models file saved, read in fine!
  • WS246 numbers: Total genes: 9,529 genes, Genes with automated descriptions: 3,362; 85,039 lines

Reporting numbers

--Currently the automated descriptions are generated for genes without a concise description

--Generate a report for numbers and place on Textpresso-dev, http://textpresso-dev.caltech.edu/concise_descriptions/

  • Report for WS246 upload, Sept/Oct, 2014:
  • Total number of automated descriptions = 3,364
  • Number of automated descriptions with homology = 2,353
  • Number of automated descriptions with process information = 1,206
  • Number of automated descriptions with function information = 2,183
  • Number of automated descriptions with component information = 244

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

Automated descriptions for C. briggsae

Automated descriptions for C. briggsae

Back To Concise Descriptions