Difference between revisions of "VariationConciseDescriptions"
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==Protein domain mutations== | ==Protein domain mutations== | ||
see Caltech group meeting [[WormBase-Caltech_Weekly_Calls_May_2015 | May 7, 2015]] <br> | see Caltech group meeting [[WormBase-Caltech_Weekly_Calls_May_2015 | May 7, 2015]] <br> | ||
− | connections between mutations and protein domains, and predict affects on function | + | connections between mutations and protein domains, and predict affects on function<br> |
+ | We currently do not capture mutations in the context of affecting a conserved amino acid - how and who would do this? Can Hinxton generate these? <br> | ||
+ | Many examples can be found with the '''Textpresso search for 'mutation conserved'''' | ||
Examples | Examples | ||
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“A mutation equivalent to sy262 G322R activates hSOS1.” | “A mutation equivalent to sy262 G322R activates hSOS1.” | ||
“...in every experiment we found that at some time point, hSOS1 C282R dis- played two- to fourfold more activity than wild-type hSOS1. In conjunction with our genetic data, these data suggest that the G322R change in C. elegans SOS-1, as well as the equivalent C282R change in hSOS1, does indeed enhance EGF-depen- dent MAPK activation.” | “...in every experiment we found that at some time point, hSOS1 C282R dis- played two- to fourfold more activity than wild-type hSOS1. In conjunction with our genetic data, these data suggest that the G322R change in C. elegans SOS-1, as well as the equivalent C282R change in hSOS1, does indeed enhance EGF-depen- dent MAPK activation.” | ||
+ | </pre> | ||
+ | |||
+ | <pre> | ||
+ | Title: The genetics of ivermectin resistance in Caenorhabditis elegans . | ||
+ | Authors: Dent JA ; Smith M ; Vassilatis DK ; Avery L | ||
+ | Journal: Proc Natl Acad Sci U S A | ||
+ | Year: 2000-03-14 | ||
+ | Doc ID: WBPaper00003954 | ||
+ | results. The region surrounding the conserved valine ( bold ) that is mutated to a glutamate in the ad1302 allele ( resulting from a T to A mutation in the second base of the V60 codon ) is shown lined up with the corresponding region in other GluCl subunits and in the rat glycine and -aminobutyric acid ( GABA ) type A- channel subunits ( 29 , 30 ) . [Field: results] | ||
+ | </pre> | ||
+ | |||
+ | |||
+ | <pre> | ||
+ | Title: POP-1 controls axis formation during early gonadogenesis in C . elegans . | ||
+ | Authors: Siegfried KR ; Kimble J | ||
+ | Journal: Development | ||
+ | Year: 2002-01 | ||
+ | Doc ID: WBPaper00005116 | ||
+ | SECTION: abstract. The pop-1 ( q624 ) allele is weakly penetrant for multiple defects and appears to be a partial loss-of-function mutation ; pop-1 ( q624 ) alters a conserved amino acid in the HMG-box DNA binding domain . [Field: abstract] | ||
+ | SECTION: discussion. This mutation alters a conserved amino acid in the HMG box DNA binding domain which is conserved specifically in TCF / LEF- 1 type HMG proteins ( Laudet et al . , 1993 ) , suggesting that the pop-1 ( q624 ) mutation may affect either recognition of the TCF / LEF-1 consensus sequence or DNA binding affinity , thereby lowering POP-1 activity . [Field: discussion] | ||
+ | SECTION: discussion. As the only mutation isolated thus far in a developmental system that changes a highly conserved amino acid in the -catenin binding domain , the pop-1 ( q645 ) missense mutation may shed new light on TCF / LEF-1 function during development . [Field: discussion] | ||
+ | SECTION: introduction. The pop-1 ( q624 ) allele is weakly penetrant for multiple defects and appears to be a partial loss-offunction mutation ; pop-1 ( q624 ) alters a conserved amino acid in the HMG-box DNA binding domain . [Field: introduction] | ||
+ | SECTION: results. The pop-1 ( q645 ) mutation carries a nucleotide substitution predicted to change an aspartic acid ( D ) to a glutamic acid ( E ) ( Fig . 2B ) ; this mutation resides within the pop-1 -catenin binding domain and alters an amino acid conserved in all known TCF / LEF-1 proteins , including nematode , fly , and vertebrate homologues . [Field: results] | ||
+ | SECTION: results. The pop-1 ( q624 ) mutation possesses a nucleotide change in the region encoding the HMG box ; the predicted amino acid change in this case also affects a conserved amino acid ( Fig . 2C ) . [Field: results] | ||
</pre> | </pre> | ||
Revision as of 21:06, 8 December 2015
Work in progress based on Ranjana's wiki for creating automated concise descriptions of genes.
Contents
- 1 Goals for variation concise descriptions
- 2 Classes of variations for concise descriptions
- 3 Querying for variation sets
- 4 Location of project-related files
- 5 Semantic categories in an Automated Description
- 6 Lesion
- 7 Protein domain mutations
- 8 Orthology/Homology
- 9 Process
- 10 References
- 11 Mapping of automated variation concise description data to OA fields
- 12 Tab-delimited file for OA insert
- 13 Directory structure for project
- 14 Inserting automated descriptions into postgres
- 15 Dumping the automated, concise and provisional descriptions
- 15.1 Dumping script
- 15.2 Script that finds genes with concise descrips that also have an automated description
- 15.3 Script that compares citace test file and Postgres for automated descriptions
- 15.4 Discontinued from WS246 upload
- 15.5 Text for Automatically_inferred tag
- 15.6 Rules for dumping the different types of descriptions in the OA
- 15.7 .ace format
- 15.8 Numbers from citace testing
- 16 Reporting numbers
- 17 Publications related to Text-mining methods
- 18 Changes/Updates for WS248
- 19 Automated descriptions for C. briggsae
- 20 Issues to address
- 21 Automated descriptions software
Goals for variation concise descriptions
This project aims to create a human-readable summary of an allele that includes a description of its lesion and effect on the gene's function and resulting phenotypes. These descriptions aim to recreate the summaries (enhanced) like those in the C. elegans I & II books, for example
e51 : paralysed kinky small irregular pharyngeal pumping able to lay eggs. ES3 ME0. NA > 30 (e450amber e312amber (non-null) e309 (see sup- 6) etc.; all similar to e51 or slightly weaker). See also e51, e328, e450, e973, e985, e2208, e2274 [C.elegansII] e51 : paralysed, kinky, small, irregular pharyngeal pumping; able to lay eggs. Ric, high acetylcholine levels; variable neuroanatomical defects.ES3 ME0. OA>30: e450amb, e312amb (non-null),e309 (suppressed by sup-6), s69, s178 etc. All alleles similar to e51 or slightly weaker.
MGI produces these summaries (do not know if they are automated): for MGI:95294
Mutations widely affect epithelial development. Null homozygote survival is strain dependent, with defects observed in skin, eye, brain, viscera, palate, tongue and other tisses. Other mutations produce an open eyed, curly whisker phenotype, while a dominant hypermorph yields a thickened epidermis.
First step -make individualized variation summaries for variation pages, then extract, combine, and shorten for corresponding gene pages.
Variation page summary
ju2 is a null allele of syd-1(F32D2.5). The ju2 lesion is a nonsense point mutation that results in a truncation of all 3 SYD-1 isoforms. ju2 results in defects in axodendritic polarity of ASI and L1 DDs, neuron morphology of ASI but not DD or VD neurons, presynaptic component localization, synaptic remodeling of VDs in adults, and backward movement resulting in coiling. ju2 animals do not show defects in neurite development or postsynaptic component localization.
e1368 is a reduction-of-function/hypomorphic allele of the insulin/IGF receptor ortholog daf-2. The e1368 lesion is a missense mutation affecting 5 of 6coding transcripts daf-2. e1368 affects many, but not all DAF-2-activity requiring processes. Specifically, e1368 disrupts DAF-2 processes of embryonic and larval development, formation of the developmentally arrested dauer larval stage (diapause), adult longevity, fat storage, salt chemotaxis learning, and stress resistance, including response to high temperature. e1368 mutants are temperature sensitive and are dauer constitutive at 22.5 deg. In addition, e1368 animals have extended life spans. e1368 animals do not show any defects in acetylcholine esterase activity, carbon dioxide avoidance, diacetyl chemotaxis, and DMPP response.
Classes of variations for concise descriptions
- Classic alleles
- Alleles with molecular data
- Alleles with only genetic data
- Alleles of genes with concise descriptions (see concise description wiki to find these)
- Other variation types
- Engineered alleles
- Integrated transgenes
- Most published alleles
- Alleles with most phenotypes
Querying for variation sets
Obtaining variation IDs and names for automated descriptions from geneace (?)
- Classic alleles
Variations with Variation_type Allele (see Variation model)
- Alleles with molecular data
***Variation_type Allele + Type_of_mutation exists
- Alleles with only genetic data
***Variation_type Allele and NO Type_of_mutation exists
- Variations of genes with concise descriptions
**Variation Affects Gene + gene exists with cns_summary table entry; acedb model Gene->Gene_info->Concise_description
- Other variation types
**Variation_type SNP, Confirmed_SNP **Variation_type Transposons, RFLPs
- Engineered variations
- Variation_type Engineered_allele
- Integrated transgenes with allele name
- Variations that have been most published
- textpresso search results
- Variations with most phenotypes
- app_variation count
on Texptresso-dev
on postgres
- The latest dump:
- Variation concise description pipeline:
- Scripts:
- Output location:
Semantic categories in an Automated Description
Molecular
- Lesion
- Gene feature
- Gene product
- Gene product domain
- Gene molecular function
Genetic
- Gene function (null, hypomorph, etc. ->app_func)
- Allele nature (recessive, dominant, etc. ->app_nature)
- Phenotype
- Affects tissue expression, subcellular localization
- Affects gene regulation
- Affects gene interaction
- Orthology to human gene mutations related to disease
Lesion
- Rationale: Molecular details
- Example:
- Model tags:
- Source files:
- Template sentence:
<Variation> is a(n) <Variation_type> in the <Species> <Gene>. This variation results in a <molecular summary> <Type_of_mutation> in the gene.
Protein domain mutations
see Caltech group meeting May 7, 2015
connections between mutations and protein domains, and predict affects on function
We currently do not capture mutations in the context of affecting a conserved amino acid - how and who would do this? Can Hinxton generate these?
Many examples can be found with the Textpresso search for 'mutation conserved'
Examples
id : WBPaper00037661 name : WBPaper00037661 title : Sequential action of Caenorhabditis elegans Rab GTPases regulates phagolysosome formation during apoptotic cell degradation. Sequencing of rab-14 in qx18 mutants revealed a C to T transition, which resulted in substitution of the Threonine at codon 67 with Methionine (ACG > ATG; T67M). This mutation affects the phosphate/Mg2+ binding domain PM3, which is conserved in all members of the Ras GTPase superfamily
title : SYD-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains, specifies axon identity in C. elegans. id : WBPaper00005543 pdf : 5543_Hallam02.pdf syd-1(GAPdeletion) mutation interferes with neurite outgrowth. construct with various missense mutations as well as a deletion in the conserved rhoGAP domain in syd-1 were made and assessed for a phenotype in transgenic animals.
id : WBPaper00027028 name : WBPaper00027028 title : Conditional dominant mutations in the Caenorhabditis elegans gene act-2 identify cytoplasmic and muscle roles for a redundant actin isoform. semidominant and embryonic-lethal mutations in the C. elegans act-2 gene. These mutations alter conserved amino acids in the predicted ATP binding pocket of actin and promote contractile instabilities and ectopic furrowing in early embryonic cells, implicating ACT-2 as a cytoplasmic actin.
Title: The Caenorhabditis elegans Iodotyrosine Deiodinase Ortholog SUP-18 Functions through a Conserved Channel SC-Box to Regulate the Muscle Two-Pore Domain Potassium Channel SUP-9 . Authors: de la Cruz IP ; Ma L ; Horvitz HR Journal: PLoS Genet Year: 2014-02 Doc ID: WBPaper00044940 SECTION: discussion. Five other sup-18 mutations affecting highly conserved residues in the NADH oxidase / flavin reductase domain also behave like null mutations , consistent with the hypothesis that SUP-18 enzymatic activity is essential for its function. SECTION: discussion. While Kvb2 knockout mice have seizures and reduced lifespans , mice carrying a catalytic null mutation in Kvb2 have a wild-type phenotype , suggesting that if an enzymatic activity for Kvb2 exists , it is functionally dispensable SUP-18 Interacts with a Two-Pore Domain K + Channel PLOS Genetics | www . plosgenetics . org 11 February 2014 | Volume 10 | Issue 2 | e1004175 in vivo [ 59 ] . IYDs across metazoan species share a similar enzymatic activity in reductive deiodination of diiodotyrosine [51], and it seems likely that SUP-18 acts similarly in C. elegans. Like mammalian IYDs, SUP-18 contains a presumptive N-terminal transmembrane domain that is required for full activity. Interestingly, the SUP-18 intracellular region lacking the transmembrane domain could still partially activate the SUP-9 channel, suggesting that membrane association is not absolutely required for SUP-9 activation by SUP-18. Membrane association is important for mammalian IYD enzymatic activities [5,52,53].
Reverse in vitro mutation analysis of elegans mutation on mammalian disease gene. Title: Introduction of a loss-of-function point mutation from the SH3 region of the Caenorhabditis elegans sem-5 gene activates the transforming ability of c-abl in vivo and abolishes binding of proline-rich ligands in vitro . Authors: Van Etten RA ; Debnath J ; Zhou H ; Casasnovas JM Journal: Oncogene Year: 1995-05-18 Doc ID: WBPaper00002191 When the n1619 mutation , which confers a lethal and highly penetrant vulvaless phenotype in C . elegans , is introduced into the c-abl SH3 domain , substituting a leucine for proline at AN amino acid number 131 , the resulting mutant transforms NIH3T3 fibroblasts with an efficiency about 10 % that of SH3-deleted c-abl .
Title: CED-9 and mitochondrial homeostasis in C . elegans muscle . Authors: Tan FJ ; Husain M ; Manlandro CM ; Koppenol M ; Fire AZ ; Hill RB Journal: J Cell Sci Year: 2008-10-15 Doc ID: WBPaper00032231 SECTION: results. This allele encodes a mutation where glycine 169 in the BH3 binding pocket is replaced with glutamate ( Fig . 4C ) ( Hengartner and Horvitz , 1994a ) , which inhibits EGL-1 from binding and triggering a conformational change in CED-9 ( del Peso et al . , 2000 ; Yan et al . , 2004 ) SECTION: results. In the gain-of-function ced-9 ( n1950sd ) allele , glycine 169 , which resides in the CED-9 BH3 binding pocket , is mutated to glutamate ( G169E ) . [Field: results, subscore: 3.00] SECTION: results. To test whether co-expression of DRP-1 modulates CED-9 via interactions with the BH3 binding pocket , we first created a construct corresponding to the ced- 9 ( n1950gf ) allele .
Schwartz, 2010, WBPaper00036020 “Since the HMT-1 polypeptide of gk161 allele lacked TMD and NBD that are required for the function of ABC transporters, we used this strain in our studies.” gk161 is hypersensitive to cadmium
WBPaper0002481 Wang 1996 identifies unc-86 binding sites in mec-3 promoter region, with accompanying evaluation of phenotypes resulting from mec-3 mutations in these regions “UNC-86 binding is blocked by certain mutations, as described above. When met-3-lacZ fusions with UNC-86 site mutations were introduced into C. elegans, mutations in Region III had a strong effect on expression, mutations in Region II had a significant effect, and mutations in Region I had no detectable effect”
WBPaper00029156 Modzelewska 2007 “the sy262 mutation lies within the Rac GEF Dbl domain , it is possible that the mutation acts through one or both of the GTPases .” “In conjunction with molecular modeling , our data suggest that the C . elegans mutation as well as an equivalent mutation in human SOS1 activate the MAPK pathway by disrupting an auto-inhibitory function of the Dbl domain on Ras activation “ “A mutation equivalent to sy262 G322R activates hSOS1.” “...in every experiment we found that at some time point, hSOS1 C282R dis- played two- to fourfold more activity than wild-type hSOS1. In conjunction with our genetic data, these data suggest that the G322R change in C. elegans SOS-1, as well as the equivalent C282R change in hSOS1, does indeed enhance EGF-depen- dent MAPK activation.”
Title: The genetics of ivermectin resistance in Caenorhabditis elegans . Authors: Dent JA ; Smith M ; Vassilatis DK ; Avery L Journal: Proc Natl Acad Sci U S A Year: 2000-03-14 Doc ID: WBPaper00003954 results. The region surrounding the conserved valine ( bold ) that is mutated to a glutamate in the ad1302 allele ( resulting from a T to A mutation in the second base of the V60 codon ) is shown lined up with the corresponding region in other GluCl subunits and in the rat glycine and -aminobutyric acid ( GABA ) type A- channel subunits ( 29 , 30 ) . [Field: results]
Title: POP-1 controls axis formation during early gonadogenesis in C . elegans . Authors: Siegfried KR ; Kimble J Journal: Development Year: 2002-01 Doc ID: WBPaper00005116 SECTION: abstract. The pop-1 ( q624 ) allele is weakly penetrant for multiple defects and appears to be a partial loss-of-function mutation ; pop-1 ( q624 ) alters a conserved amino acid in the HMG-box DNA binding domain . [Field: abstract] SECTION: discussion. This mutation alters a conserved amino acid in the HMG box DNA binding domain which is conserved specifically in TCF / LEF- 1 type HMG proteins ( Laudet et al . , 1993 ) , suggesting that the pop-1 ( q624 ) mutation may affect either recognition of the TCF / LEF-1 consensus sequence or DNA binding affinity , thereby lowering POP-1 activity . [Field: discussion] SECTION: discussion. As the only mutation isolated thus far in a developmental system that changes a highly conserved amino acid in the -catenin binding domain , the pop-1 ( q645 ) missense mutation may shed new light on TCF / LEF-1 function during development . [Field: discussion] SECTION: introduction. The pop-1 ( q624 ) allele is weakly penetrant for multiple defects and appears to be a partial loss-offunction mutation ; pop-1 ( q624 ) alters a conserved amino acid in the HMG-box DNA binding domain . [Field: introduction] SECTION: results. The pop-1 ( q645 ) mutation carries a nucleotide substitution predicted to change an aspartic acid ( D ) to a glutamic acid ( E ) ( Fig . 2B ) ; this mutation resides within the pop-1 -catenin binding domain and alters an amino acid conserved in all known TCF / LEF-1 proteins , including nematode , fly , and vertebrate homologues . [Field: results] SECTION: results. The pop-1 ( q624 ) mutation possesses a nucleotide change in the region encoding the HMG box ; the predicted amino acid change in this case also affects a conserved amino acid ( Fig . 2C ) . [Field: results]
Orthology/Homology
see Caltech group meeting May 7, 2015
- to connect conserved/syntenic mutations
- link elegans gene variations and phenotypes to homologous human disease gene variations
- to link elegans mutations as a disease model ex. pdr-1 mutations used to model juvenile parkinsons
use ortholog(s) of gene defined by Generation_of_automated_descriptions#Orthology.2FHomology Orthology, Homology and Paralog data in WormBase
Template of an Orthology sentence
- <Worm Gene> is an ortholog of <human gene>.
- Similar or identical mutations in the <human gene> has been associated with <disease>.
Rules for orthology sentence construction
How to pick orthologs for the description
use human gene that is associated with disease and has mutation information
Process
- Rationale:
- Template for a process sentence
<Variation> affects <Gene>'s role in <process>;
- Source file for Process data
*Source 1: 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 **this file is one build behind, compared to release label for the phenotype2go annotations *Source 2: (from WS250): phenotype2go file, these automated annotations are now 'IEAs', but will be treated like IMPs, if they have the 'WBPhenotype:XXXXXXX' in column 8 (with) **this file is current with the release label for the phenotype2go annotations **Source 1 and 2 will have redundant annotations but these will get resolved **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''': Only apply source from IMP GO terms, if variation is listed *'''Rule 4''': 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 5''': No exclusions as of 07.07.2014, leave in reproduction: *'''Rule 6''' 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 7''': 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 8''': 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 9''': 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 10''': 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.
References
WBPaper00047004 title : Comparative mapping of the 22q11.2 deletion region and the potential of simple model organisms. Guna_2015
==Molecular function/identity== ====Source file for molecular function data==== **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''': Ignore all GO terms with the tag 'is_obsolete: true' *'''Rule 2''': Exclusion list: **Ignore the term 'protein binding' **Ignore the term 'binding' *'''Rule 3''': For identical GO terms with both experimental (EXP, IDA, IPI, IMP, IGI, IEP) and computational evidence codes (ISS, IEA), keep only the non-redundant GO terms from experimental evidence and ignore the computational evidence codes. *'''Rule 4''': Order the experimental GO terms first in the sentence followed by ISS and IEA terms. *'''Rule 5''': 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 6''': 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 7''': If a binding term is present add the word 'activity' to it. *'''Rule 8''': 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 9''': 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 10''' 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 11''': If a GO term has a comma in it, then add a comma after this GO term and the next ‘and’. ==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 ====Rules for sub-cellular localization sentence construction==== *'''Rule 1''': Ignore GO terms with the tag 'is_obsolete: true' in the obo file *'''Rule 2''': Ignore all IEA and ISS GO terms, use only non-IEA, non-ISS GO terms *'''Rule 4''': Ignore IBA and IBD GO terms (PAINT annotations) *'''Rule 5''': For identical GO terms with both experimental (EXP, IDA, IPI, IMP, IGI, IEP) and computational evidence codes (ISS, IEA), keep only the non-redundant GO terms from experimental evidence and ignore the computational evidence codes. *'''Rule 6''': 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; *'''Rule 7''': For the GO term 'intracellular [IEA]' structure of the sentence will be different, use 'is intracellular'. **Eg.1 WBGene00089742 **PPA00188 is an ortholog of C. elegans T26A5.8; based on protein domain information, PPA00188 is predicted to have sequence-specific DNA binding activity and protein heterodimerization activity and is intracellular. ==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'; treat 'Certain' and 'Partial' equally; also use all expression data with no qualifiers as well, qualifiers were added recently. '''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. ==Preliminary results== These descriptions are based on Homology predictions and the GO annotations for Process, Component and Function: <pre style="white-space: pre-wrap; white-space: -moz-pre-wrap; white-space: -pre-wrap; white-space: -o-pre-wrap; word-wrap: break-word"> *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 variation concise description data to OA fields
OA field number |
OA field name | Data to be inserted | Example of data to be inserted |
Required or Not | OA table name |
---|---|---|---|---|---|
1 | WBVariation | Variation | WBVar00145853 OR gk448 | Required | vcd_variation |
2 | Species | Species | Onchocerca volvulus | Required | vcd_species |
3 | Curator | Name of Curator | James Done(first then replace with) Karen Yook (insert for all rows) |
Required | vcd_curator |
4 | Curator History | Name of Curator | same as pgid (insert for all rows) |
Required | vcd_curhistory |
5 | Description Type | Automated_concise_description (insert for all rows) |
Automated_concise_description | Required | vcd_desctype |
6 | Description Text | the automated concise description | asp-19 encodes an ortholog... | Required | vcd_desctext |
7 | Reference | WBPaper | WBPaper00026979 | Required | vcd_paper |
8 | Accesssion Evidence | For Homology, for elegans, use ENSEMBL Gene ID, for non-elegans species use WBGeneID For Process, Function, use InterPro ID |
For elegans: ENSEMBL:ENSG00000103257 (previously used the protein ENSEMBL protein ids) and INTERPRO:IPR002293 For non-elegans species: WBGene00007443 and INTERPRO:IPR002293 (comma separate multiple values) |
Not required | con_accession |
9 | Last Updated | Date when the descriptions were last generated |
2014-09-11 | Required | vcd_lastupdate |
10 | pgid | pgid | 1149 (Postgres will generate) |
Required |
Tab-delimited file for OA insert
- One tab-delimited file per species
- Order of the data will be: WBGene, Date, Paper, Accession_evidence, Automated_concise_description, Species, 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
Directory structure for project
- http://textpresso-dev.caltech.edu/concise_descriptions/ Top level parent directory for project
- http://textpresso-dev.caltech.edu/concise_descriptions/production_release.txt Indicates what release the file corresponds to
- http://textpresso-dev.caltech.edu/concise_descriptions/species.txt Indicates the different species we are producing description files for
- http://textpresso-dev.caltech.edu/concise_descriptions/release/WS247/c_elegans/descriptions/OA_concise_descriptions.WS247.txt WS247 elegans file for import into OA
Inserting automated descriptions into postgres
Populating script
Run the script to populate from here: /home/acedb/ranjana/concise_testing/populate_automated_concise_descriptions.pl
Script actually at: /home/postgres/work/pgpopulation/concise_description/20140909_automated_concise/populate_automated_concise_descriptions.pl
Script looks at http://textpresso-dev.caltech.edu/concise_descriptions/production_release.txt for release number and
http://textpresso-dev.caltech.edu/concise_descriptions/species.txt for the different species
Script gets data from the following URL for each of the species: For elegans: http://textpresso-dev.caltech.edu/concise_descriptions/release/WS247/c_elegans/descriptions/OA_concise_descriptions.WS247.txt
For briggsae: http://textpresso-dev.caltech.edu/concise_descriptions/release/WS247/c_briggsae/descriptions/OA_concise_descriptions.WS247.txt
and so on.
When populating for each OA row that has con_desctype set to 'Automated_concise_description', it will delete from these tables :
- con_wbgene
- con_species
- con_curator
- con_curhistory
- con_desctext
- con_paper
- con_accession
- con_inferredauto
- 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
For testing on Mangolassi
Both populating and dumping scripts at:/home/acedb/ranjana/concise_testing
For the polulating script always redirect output to a file: populate_automated_concise_descriptions.pg.<date>
Dumping the automated, concise and provisional descriptions
Dumping script
- 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
- Concise descriptions dumper at /home/postgres/work/citace_upload/concise/dump_concise.pl
- /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace
Script that finds genes with concise descrips that also have an automated description
On Tazendra and Mangolassi: /home/acedb/ranjana/concise_testing/find_concise_with_automated.pl
Script that compares citace test file and Postgres for automated descriptions
Location:/home/acedb/ranjana/concise_testing/compare_concise_postgres_vs_acefile.pl
- Needs a 'citace_genes_with_automated.ace' file which is the .ace export of all genes in citace with the 'Automated_description' tag (I use Query buildr to do this query and then export the 'Names' to a file 'citace_genes_with_automated.ace').
- Compares the output from citace (from testing concise_dump_new.ace in empty citace database on Maya) of genes with automated tag, to postgres data, also outputs if a gene has a concise description (which would not be dumped so not in .ace file, but in Postgres).
- For the WS247 upload, 1 gene not accounted for, WBGene00020108, which has been merged into a dead gene?
Discontinued from WS246 upload
- concise cronjob is on the acedb account : 0 2 * * thu /home/acedb/kimberly/citace_upload/concise/wrapper.pl (turned off for now)
- It creates a file at: /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace
- which you can see on the web at:http://tazendra.caltech.edu/~postgres/cgi-bin/data/concise_dump_new.ace
- Then on spica, login, go to the Data_for_citace/Data_from_Kimberly directory, remove the existing file, and upload the latest file using: wget http://tazendra.caltech.edu/~postgres/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 <WS246> version of WormBase.
Rules for dumping the different types of descriptions in the OA
.ace format
List of tags to be dumped:
- Automated_description
- Paper_evidence
- Accession_evidence
- Date_last_updated
- Inferred_automatically
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
- 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
Changes/Updates for WS248
- Changes to Orthology,
Automated descriptions for C. briggsae
Automated descriptions for C. briggsae
Issues to address
- 1. For the non-elegans species, need to use the WBGeneID as Accession_evidence, so can we use our own database, and do: Accession_evidence "WormBase" "WBGene00005678" (not done)
- 2. For non-elegans species, need to add in elegans gene experimental data, but with multiple orthologs, which do we pick? (done, using only the common GO terms for orthologs)
- 3. Gene names should be pulled and mapped to the Gene IDs only from the gene names file, not from the source files of orthology or GO (will be addressed for WS250)
- 4. For WS250, check that the gene names are (somewhat) current; corrected mel-47 to tofu-6 by hand for WS249.