Difference between revisions of "VariationConciseDescriptions"
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</pre> | </pre> | ||
− | == | + | ==Source files for project== |
− | |||
*obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation | *obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation | ||
*obo_data_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_data_variation | *obo_data_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_data_variation | ||
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*gin_seqname tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | *gin_seqname tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | ||
− | ===Building | + | ==Building sentences== |
+ | ===Building Molecular sentence 1 === | ||
====Template for molecular sentence 1==== | ====Template for molecular sentence 1==== | ||
<variation> is a <app_nature> allele of <gene>. | <variation> is a <app_nature> allele of <gene>. | ||
− | + | *Ex. "ju2 is a null allele of syd-1(F32D2.5)" | |
− | + | *Ex. "e1368 is a reduction-of-function/hypomorphic allele of daf-2." | |
− | ====Sources for molecular sentence | + | ====Sources for molecular sentence 2==== |
* Source 1: geneace file on postgres | * Source 1: geneace file on postgres | ||
** tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | ** tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | ||
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*Source 3: postgres table app_function | *Source 3: postgres table app_function | ||
− | ====Template for Molecular sentence | + | ===Building Molecular sentence 2A - gene features=== |
− | The <variation> is a <Molecular_change> | + | Gene features include DNA binding sites, promoters, UTRs, splice sites |
− | + | ====Template for Molecular sentence -gene features==== | |
+ | The <variation> is a <Molecular_change> in <gene feature> in <gene>. | ||
+ | *Ex. tm3467 is a deletion mutation in a splice acceptor site in supr-1. (WBPaper00045690) | ||
+ | ====source tags==== | ||
+ | #Molecular_change tags: | ||
+ | <pre> | ||
+ | Splice_site Donor Text #Evidence | ||
+ | Acceptor Text #Evidence | ||
+ | Frameshift Text #Evidence // added sdm | ||
+ | </pre> | ||
+ | |||
+ | ===Building Molecular sentence 2B - gene processing=== | ||
+ | Gene processing effects include, truncation, frameshifts | ||
+ | ====Template for Molecular sentence -gene processing==== | ||
+ | The <variation> is a <Molecular_change> in <gene feature> in <gene>. | ||
+ | *Ex. n3763 is a frameshift mutation in lin-35. (WBPaper00027336) | ||
+ | *Ex. n767 is a silent mutation in lin-15. (WBPaper00001182) | ||
+ | ====source tags==== | ||
+ | #Molecular_change tags: | ||
+ | <pre> | ||
+ | Silent Text #Evidence | ||
+ | Splice_site Donor Text #Evidence | ||
+ | Acceptor Text #Evidence | ||
+ | Frameshift Text #Evidence // added sdm | ||
+ | Readthrough Text #Evidence // klh WS228 | ||
+ | </pre> | ||
+ | |||
+ | ===Building Molecular sentence 2C - protein domains=== | ||
+ | Protein domains include catalytic sites, binding domains, activation domains etc. | ||
+ | ====Template for Molecular sentence -protein domains==== | ||
+ | The <variation> is a <Molecular_change> in the <protein domain> of <gene>. | ||
+ | *Ex. gk291 is a deletion mutation in the PTB domain of dab-1. (WBPaper00031546) | ||
+ | |||
+ | |||
====Sources for molecular sentence 2==== | ====Sources for molecular sentence 2==== | ||
* Source 1: geneace file on postgres | * Source 1: geneace file on postgres | ||
**tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | **tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace | ||
− | * Source 2: TBD for | + | * Source 2: TBD for associated domain |
Variation description tags needed for the above text: | Variation description tags needed for the above text: | ||
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Opal_UGA Text #Evidence | Opal_UGA Text #Evidence | ||
Missense Text #Evidence // text fields stored details of codon change | Missense Text #Evidence // text fields stored details of codon change | ||
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</pre> | </pre> | ||
− | * | + | =====problems===== |
+ | *coding vs noncoding genes | ||
+ | *mutation in noncoding area of gene | ||
+ | *mutation affects isoforms differently | ||
+ | *only use variations mapped onto human proteins, rather than other way around - keep in sync with with other projects, also limits sentence to a subset of isoforms? | ||
+ | *..."that is or is not conserved in humans." can only use under limited situations, orthology needs to be done. | ||
===Building gene process summary sentences=== | ===Building gene process summary sentences=== | ||
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WB WBGene00017066 maco-1 GO:0023041 WB_REF:WBPaper00038428|PMID:21589894 IMP WB:WBVar00597666|WB:WBVar00597667 P D2092.5 gene taxon:6239 20110824 WB | WB WBGene00017066 maco-1 GO:0023041 WB_REF:WBPaper00038428|PMID:21589894 IMP WB:WBVar00597666|WB:WBVar00597667 P D2092.5 gene taxon:6239 20110824 WB | ||
</pre> | </pre> | ||
+ | |||
====Rules for Process sentence construction==== | ====Rules for Process sentence construction==== | ||
*'''Rule 1: '''Ignore all lines that do no have "IMP" in column 7 | *'''Rule 1: '''Ignore all lines that do no have "IMP" in column 7 | ||
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*'''nj34''' affects '''maco-1''' function in chemotaxis and neuronal signal transduction | *'''nj34''' affects '''maco-1''' function in chemotaxis and neuronal signal transduction | ||
− | ===Building Phenotype Observed summary sentences=== | + | ===Building Phenotype Observed summary sentences using phenotype_association file=== |
====Template for Phenotype observed sentences==== | ====Template for Phenotype observed sentences==== | ||
<Variation> results in (defects, alterations) in <phenotype(s)>. <br> | <Variation> results in (defects, alterations) in <phenotype(s)>. <br> | ||
− | + | Ex: "e1368 disrupts DAF-2 processes of embryonic and larval development, | |
formation of the developmentally arrested dauer larval stage (diapause), adult | formation of the developmentally arrested dauer larval stage (diapause), adult | ||
longevity, fat storage, salt chemotaxis learning, and stress resistance, including | longevity, fat storage, salt chemotaxis learning, and stress resistance, including | ||
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</pre> | </pre> | ||
− | ====Rules for phenotype sentence construction==== | + | ====Rules for phenotype sentence construction using postgres tables==== |
− | '''Rule 1: '''For | + | '''Rule 1:''' For lines that does not contain a value in column 4, |
− | *variation(column 6 or 8), | + | *extract variation(column 6 or 8), |
*phenotype (column 5) | *phenotype (column 5) | ||
*paper(column 6) | *paper(column 6) | ||
*ex. "WB:WBVar00143947" "WBPhenotype:0001861" "WBPaper00041295" | *ex. "WB:WBVar00143947" "WBPhenotype:0001861" "WBPaper00041295" | ||
*Map WBVariationID to Variation public_name using obo_name_variation<br> | *Map WBVariationID to Variation public_name using obo_name_variation<br> | ||
− | * Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo<br> | + | *Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo<br> |
− | '''Rule 2: '''When more than one variation exists in a line create a new line and use only one variation, with same phenotype, NOT(if exists), and paper as original line<br> | + | '''Rule 2:''' When more than one variation exists in a line create a new line and use only one variation, with same phenotype, NOT(if exists), and paper as original line<br> |
− | '''Rule 3: '''Pool all phenotypes for a given variation, comma separate<br> | + | '''Rule 3:''' Pool all phenotypes for a given variation, comma separate<br> |
− | '''Rule 4: '''If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s) | + | '''Rule 4:''' If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s)<br> |
− | '''Rule 5: '''Remove 'variant' from public names that have them<br> | + | |
+ | |||
+ | ===Building Phenotype Observed summary sentences using phenotype_association file=== | ||
+ | |||
+ | ====Template for Phenotype observed sentences==== | ||
+ | <Variation> results in (defects, alterations) in <phenotype(s)>. <br> | ||
+ | Ex: "e1368 effects embryonic and larval development, | ||
+ | formation of the developmentally arrested dauer larval stage (diapause), adult | ||
+ | longevity, fat storage, salt chemotaxis learning, stress resistance, and | ||
+ | response to high temperature. In addition, mutants have extended life spans. " | ||
+ | |||
+ | ====Source files Phenotype Observed data==== | ||
+ | Source 1 postgres app tables: | ||
+ | <pre> | ||
+ | app_term | ||
+ | app_variation | ||
+ | app_paper | ||
+ | </pre> | ||
+ | *phenotype ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest release) | ||
+ | *obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation | ||
+ | |||
+ | ====Rules for phenotype sentence construction==== | ||
+ | '''Rule 1:''' | ||
+ | *extract variation - app_variation | ||
+ | *phenotype - app_term | ||
+ | *paper - app_paper | ||
+ | *ex. "WB:WBVar00143947" "WBPhenotype:0001861" "WBPaper00041295" | ||
+ | *Map WBVariationID to Variation public_name using obo_name_variation<br> | ||
+ | *Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo<br> | ||
+ | '''Rule 2:''' When more than one variation exists in a line create a new line and use only one variation, with same phenotype, NOT(if exists), and paper as original line<br> | ||
+ | '''Rule 3:''' Pool all phenotypes for a given variation, comma separate<br> | ||
+ | '''Rule 4:''' If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s)<br> | ||
+ | '''Rule 5:''' Remove 'variant' from public names that have them<br> | ||
+ | |||
+ | ====Rules for specific phenotype terms==== | ||
+ | '''Rule 1:''' For all terms that contain 'variant' remove 'variant' from public names that have them<br> | ||
+ | '''Rule 2:''' For the following terms: | ||
+ | * WBPhenotype:0000061 - extended life span | ||
+ | * WBPhenotype:0001171 - shortened life span | ||
+ | ** add an "s" to the end of the term public name | ||
+ | ** use the phrasing "In addition, mutants have extended life spans." | ||
+ | * WBPhenotype:0001838 - drug induced gene expression variant | ||
+ | * WBPhenotype:0001871 - drug induced life span variant | ||
+ | * WBPhenotype:0001872 - drug induced locomotion variant | ||
+ | ** change "induced" to "influenced" | ||
+ | * Terms that end in "early emb" | ||
+ | ** replace "early emb" in the term with "in the early embryo" | ||
+ | ** for term WBPhenotype:0001185 "embryonic developmental delay early emb", remove "embryonic" | ||
+ | ** for term WBPhenotype:0001186 "embryo delayed at pronuclear contact early emb", remove the first term "embryo" | ||
+ | |||
+ | ===Building Phenotype Attribute summary sentences=== | ||
+ | ====Template for Phenotype Attribute summary sentences==== | ||
+ | <variation> is <app attribute>, <app attribute> <app_term> | ||
+ | *Ex. "s1019 is cold-sensitive, maternal effect mid larval lethal;" | ||
+ | |||
+ | <variation> is <app attribute> <app_term> at <app_heat_temp> OR <variation> is <app attribute> <app term> at < | ||
+ | *Ex. "e1368 is temperature sensitive dauer constitutive at 22.5 deg C;" | ||
+ | |||
+ | <variation> is <app attribute> for all phenotypes at <app_heat_degree> OR <variation> is <app attribute> for all phenotypes at <app_cold_degree> | ||
+ | *Ex. "oj21 is temperature sensitive for all phenotypes at 25 deg C; " | ||
+ | |||
+ | <variation> is <app_mat_effect> <app_term> | ||
+ | *Ex. "oj21 is maternal effect embryonic lethal;" | ||
+ | |||
+ | ====Source for Phenotype Attribute sentence==== | ||
+ | postgres app tables | ||
+ | |||
+ | ====Rules for Phenotype Attribute summary sentences==== | ||
+ | '''Rule 1:''' when there are more than one phentoype attribute sentences, use the generic "animals" instead of repeating the allele name | ||
+ | *Ex "oj21 is temperature sensitive for all phenotypes at 25 deg C; oj21 is maternal effect embryonic lethal; animals are 100% sterile at 25 degrees C;" | ||
===Building Phenotype NOT Observed summary sentences=== | ===Building Phenotype NOT Observed summary sentences=== | ||
====Template for Phenotype NOT observed sentences==== | ====Template for Phenotype NOT observed sentences==== | ||
<Allele> does not show (defects, alterations) in <NOT phenotype(s)>. | <Allele> does not show (defects, alterations) in <NOT phenotype(s)>. | ||
− | + | *Ex. "e1368 animals do not show any defects in acetylcholine esterase activity, carbon dioxide avoidance, diacetyl chemotaxis, and DMPP response." | |
====Source files Phenotype Observed data==== | ====Source files Phenotype Observed data==== | ||
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WB WBGene00000898 daf-2 WBPhenotype:0000637 WB_REF:WBPaper00038179 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB | WB WBGene00000898 daf-2 WBPhenotype:0000637 WB_REF:WBPaper00038179 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB | ||
</pre> | </pre> | ||
− | ====Rules for phenotype sentence construction | + | ====Rules for phenotype sentence construction==== |
'''Rule 1:''' For each line that contains (NOT) value in column 4, extract | '''Rule 1:''' For each line that contains (NOT) value in column 4, extract | ||
*variation(column 6 or 8), | *variation(column 6 or 8), | ||
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'''Rule 5:''' Remove 'variant' from public names that have them<br> | '''Rule 5:''' Remove 'variant' from public names that have them<br> | ||
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=== Building Disease Orthology summary sentences=== | === Building Disease Orthology summary sentences=== | ||
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==Prioritizing variations for automated descriptions== | ==Prioritizing variations for automated descriptions== | ||
− | * Classic alleles | + | *Classic alleles - Variations with Variation_type Allele (see [[WormBase_Model:Variation | Variation model]]) |
− | + | **Alleles with molecular data => Variation_type Allele + Type_of_mutation exists | |
− | **Alleles with molecular data | + | **Alleles with only genetic data => Variation_type Allele and NO Type_of_mutation exists |
− | + | *Variations of genes with concise descriptions | |
− | **Alleles with only genetic data | + | **Variation Affects Gene + gene exists with cns_summary table entry; acedb model Gene->Gene_info->Concise_description |
− | + | *Other variation types | |
− | * Variations of genes with concise descriptions | + | **Variation_type SNP, Confirmed_SNP |
− | + | **Variation_type Transposons, RFLPs | |
− | * Other variation types | ||
− | |||
− | |||
*Engineered variations | *Engineered variations | ||
− | ** Variation_type Engineered_allele | + | **Variation_type Engineered_allele |
* Integrated transgenes with allele name | * Integrated transgenes with allele name | ||
− | * Variations that have been most published | + | *Variations that have been most published |
**textpresso search results | **textpresso search results | ||
− | * Variations with most phenotypes | + | *Variations with most phenotypes |
**app_variation count | **app_variation count | ||
− | == | + | ==Orthology/ Conserved domain mutations== |
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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<br> | connections between mutations and protein domains, and predict affects on function<br> | ||
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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+ | 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 | binding domain PM3, which is conserved in all members of the Ras GTPase superfamily | ||
− | |||
− | + | Sentences to make: | |
− | + | *Molecular sentence 2: "qx18 encodes a C to T transition, T67M which affects the phosphate/Mg2+ binding domain PM3" | |
− | + | *Orthology sentence: "The phosphate/Mg2+ binding domain PM3 is conserved in all members of the Ras GTPase superfamily" | |
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</pre> | </pre> | ||
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Doc ID: WBPaper00002191 | 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 . | 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 . | ||
+ | |||
+ | Sentence to make: | ||
+ | *Molecular sentence 2: "n1619 encodes a L131P substitution in the c-abl SH3 domain" | ||
</pre> | </pre> | ||
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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. 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 . | 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 . | ||
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− | + | Sentence to make: | |
− | + | *Molecular sentence 2: "n1950 encodes a G169E change in the BH3 binding pocket of CED-9" | |
− | |||
− | |||
</pre> | </pre> | ||
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“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 “ | “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.” | “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- | + | “...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-dependent MAPK activation.” |
+ | |||
+ | Sentence to make: | ||
+ | *Molecular sentence 2: "sy262 encodes a G33R mutation in the Rac GEF Dbl domain and is equivalent to a C282R change in the human hSOS1." | ||
+ | *Orthology sentence: "The sy262 G33R mutation is equivalent to a C282R change in the human hSOS1." | ||
</pre> | </pre> | ||
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Doc ID: WBPaper00003954 | 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] | 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] | ||
+ | |||
+ | Sentence to make: | ||
+ | *Molecular sentence 2: "ad1302 encodes a Val to Glu change." | ||
+ | *Orthology sentence: "ad1302 affects a region that is conserved in GluCl subunits as well as in rat glycine and GABA type A-channel subunits." | ||
</pre> | </pre> | ||
− | |||
<pre> | <pre> | ||
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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. 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: 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- | + | SECTION: introduction. 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: 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 ( 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] | 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] | ||
+ | |||
+ | Sentence to make: | ||
+ | *Molecular sentence 2: "q624 encodes a D to E change in the catenin binding domain" | ||
+ | *Orthology sentence: "q624 affects a conserved amino acid in the HMG-box DNA binding domain specifically in TCF/LEF-1 type HMG proteins" | ||
</pre> | </pre> | ||
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#Molecular sentence 1 | #Molecular sentence 1 | ||
#Molecular sentence 2 | #Molecular sentence 2 | ||
+ | #Disease/Orthology | ||
#Process | #Process | ||
#Phenotype observed | #Phenotype observed | ||
+ | #Phenotype attribute | ||
#Phenotype NOT observed | #Phenotype NOT observed | ||
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==Postgres sources == | ==Postgres sources == | ||
<pre> | <pre> | ||
− | Source files for | + | Source files for phenotype attribute data for variation concise description |
− | * | + | *OA (app) tables: |
− | * | + | **app_variation |
+ | **app_term | ||
+ | app_paper, app_easescore, app_mmateff, app_hmateff, app_molecule, app_anatomy, app_lifestage, app_penetrance, app_mat_effect, app_temperature, app_cold_degree, app_heat_degree, app+pat_effect | ||
+ | app_haplo, app_cold_sens, app_heat_sens | ||
+ | <pre> | ||
+ | need to adapt for variation concise description | ||
**for all these tables where exp_endogenous table value 'endogenous', grab the exp_gene, WBGeneXXXXXXXX | **for all these tables where exp_endogenous table value 'endogenous', grab the exp_gene, WBGeneXXXXXXXX | ||
**exp_name, values look like Expr1005. | **exp_name, values look like Expr1005. | ||
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**exp_paper for paper | **exp_paper for paper | ||
**exp_qualifier for the qualifiers 'certain', 'uncertain' and 'partial'. | **exp_qualifier for the qualifiers 'certain', 'uncertain' and 'partial'. | ||
− | + | ||
</pre> | </pre> | ||
Latest revision as of 01:38, 2 March 2016
Contents
- 1 Useful links
- 2 Variation concise descriptions
- 3 Source files for project
- 4 Building sentences
- 4.1 Building Molecular sentence 1
- 4.2 Building Molecular sentence 2A - gene features
- 4.3 Building Molecular sentence 2B - gene processing
- 4.4 Building Molecular sentence 2C - protein domains
- 4.5 Building gene process summary sentences
- 4.6 Building Phenotype Observed summary sentences using phenotype_association file
- 4.7 Building Phenotype Observed summary sentences using phenotype_association file
- 4.8 Building Phenotype Attribute summary sentences
- 4.9 Building Phenotype NOT Observed summary sentences
- 4.10 Building Disease Orthology summary sentences
- 5 Examples for concise descriptions for variations of different types
- 6 Prioritizing variations for automated descriptions
- 7 Orthology/ Conserved domain mutations
- 8 Location of project-related files
- 9 Order of sentences
- 10 Postgres sources
- 11 Preliminary results
- 12 Mapping of automated variation concise description data to OA fields
- 13 Tab-delimited file for OA insert
- 14 Directory structure for project
- 15 Inserting automated descriptions into postgres
- 16 Dumping to .ace
- 17 Tracking progress
- 18 Changes/Updates for each release
- 19 Issues to address
- 20 Automated descriptions software
- 21 Publications related to Text-mining methods
Useful links
app tables
variation model
Ranjana's wiki for creating automated concise descriptions of genes.
geneace upload info
geneace upload of nongene info
Variation concise descriptions
Human-readable summaries of alleles that include a description of its lesion, its effect on the gene's function, and resulting phenotypes. These descriptions aim to recreate summaries like those in the C. elegans I & II books and enhance them with up to date data. A first step is to make and display summaries for each variation; second step is to extract info and combine the summaries of a gene's variations and display them on the corresponding gene pages.
From C. elegans II 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.
Sample allele summaries:
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 6 coding 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.
Source files for project
- obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation
- obo_data_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_data_variation
- phenotype_ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest release)
- phenotype_association ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_association.WS251.wb (correct for latest release)
- gene_association ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/gene_association.WS251.wb.c_elegans (correct for latest release)
- gin_seqname tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace
Building sentences
Building Molecular sentence 1
Template for molecular sentence 1
<variation> is a <app_nature> allele of <gene>.
- Ex. "ju2 is a null allele of syd-1(F32D2.5)"
- Ex. "e1368 is a reduction-of-function/hypomorphic allele of daf-2."
Sources for molecular sentence 2
- Source 1: geneace file on postgres
- tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace
- Source 2: gin_seqname.pg
- tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace
- Source 3: postgres table app_function
Building Molecular sentence 2A - gene features
Gene features include DNA binding sites, promoters, UTRs, splice sites
Template for Molecular sentence -gene features
The <variation> is a <Molecular_change> in <gene feature> in <gene>.
- Ex. tm3467 is a deletion mutation in a splice acceptor site in supr-1. (WBPaper00045690)
source tags
- Molecular_change tags:
Splice_site Donor Text #Evidence Acceptor Text #Evidence Frameshift Text #Evidence // added sdm
Building Molecular sentence 2B - gene processing
Gene processing effects include, truncation, frameshifts
Template for Molecular sentence -gene processing
The <variation> is a <Molecular_change> in <gene feature> in <gene>.
- Ex. n3763 is a frameshift mutation in lin-35. (WBPaper00027336)
- Ex. n767 is a silent mutation in lin-15. (WBPaper00001182)
source tags
- Molecular_change tags:
Silent Text #Evidence Splice_site Donor Text #Evidence Acceptor Text #Evidence Frameshift Text #Evidence // added sdm Readthrough Text #Evidence // klh WS228
Building Molecular sentence 2C - protein domains
Protein domains include catalytic sites, binding domains, activation domains etc.
Template for Molecular sentence -protein domains
The <variation> is a <Molecular_change> in the <protein domain> of <gene>.
- Ex. gk291 is a deletion mutation in the PTB domain of dab-1. (WBPaper00031546)
Sources for molecular sentence 2
- Source 1: geneace file on postgres
- tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace
- Source 2: TBD for associated domain
Variation description tags needed for the above text:
- Molecular_change tags:
Nonsense UNIQUE Amber_UAG Text #Evidence Ochre_UAA Text #Evidence Opal_UGA Text #Evidence Missense Text #Evidence // text fields stored details of codon change
problems
- coding vs noncoding genes
- mutation in noncoding area of gene
- mutation affects isoforms differently
- only use variations mapped onto human proteins, rather than other way around - keep in sync with with other projects, also limits sentence to a subset of isoforms?
- ..."that is or is not conserved in humans." can only use under limited situations, orthology needs to be done.
Building gene process summary sentences
Template for a process sentence
<Variation> affects <Gene> function in <GO>.
Example:
- lf29 affects polk-1 function in error-prone translesion synthesis.
- bp501 affects atg-4.1 function in autophagy.
- ns260 affects ttx-1 function in embryo development ending in birth or egg hatching
- ns235 affects ttx-1 function in the regulation of transcription from RNA polymerase II promoter
- gg91 affects nrde-2 function in chromatin silencing by small RNA
Source files for process sentences
- obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation
- gene_association ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/gene_association.WS251.wb.c_elegans (correct for latest release)
- gin_seqname tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace
Gene association file:
WB WBGene00006831 unc-104 GO:0048490 WB_REF:WBPaper00045884|PMID:25329901 IMP WB:WBVar02141295 P C52E12.2|klp-1 gene taxon:6239 20141212 WB WB WBGene00019126 sam-4 GO:1903744 WB_REF:WBPaper00045884|PMID:25329901 IMP WB:WBVar02125688 P F59E12.11 gene taxon:6239 20141212 WB WB WBGene00017696 polk-1 GO:0042276 WB_REF:WBPaper00041255|PMID:22761594 IMP WB:WBVar01473736 P F22B7.6 gene taxon:6239 20150611 WB WB WBGene00013595 atg-4.1 GO:0006914 WB_REF:WBPaper00041282|PMID:22767594 IMP WB:WBVar01473704 P Y87G2A.3 gene taxon:6239 20140724 WB WB WBGene00006652 ttx-1 GO:0009792 WB_REF:WBPaper00040681|PMID:22298710 IMP WB:WBVar00603928 P Y113G7A.6 gene taxon:6239 20140408 WB WB WBGene00006652 ttx-1 GO:0045944 WB_REF:WBPaper00040681|PMID:22298710 IMP WB:WBVar00603924 P Y113G7A.6 gene taxon:6239 20140408 WB has_regulation_target<WB:WBGene00006894>,occurs_in<WBbt:0006754>,happens_during<GO:0009408> WB WBGene00011333 nrde-2 GO:0031048 WB_REF:WBPaper00040602|PMID:22231482 IMP WB:WBVar00601048 P T01E8.5 gene taxon:6239 20150715 WB WB WBGene00017066 maco-1 GO:0006935 WB_REF:WBPaper00038428|PMID:21589894 IMP WB:WBVar00597666|WB:WBVar00597667 P D2092.5 gene taxon:6239 20110823 WB WB WBGene00017066 maco-1 GO:0023041 WB_REF:WBPaper00038428|PMID:21589894 IMP WB:WBVar00597666|WB:WBVar00597667 P D2092.5 gene taxon:6239 20110824 WB
Rules for Process sentence construction
- Rule 1: Ignore all lines that do no have "IMP" in column 7
- Rule 2: Map column 8 WBVariation to <allele public name> -
*use obo_name_variation.pg at tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace *WBVarID is in first column of geneace file, public_name is second column of geneace file
- Rule 3: When there are more than one WBVarIDs in column 8, map other WBVarIDs and create a separate summary for those objects
- Rule 4: Map column 5 GO:ID to GO name -
*use obo_goidprocess at tazendra /home/postgres/work/pgpopulation/obo_oa_ontologies
obo_goidprocess looks like:
GO:ID in line id: <GO:ID#######> name in line name: <GO name> If GO:term name starts with a qualifiers "negative" or "positive", replace qualifier with "the"
Example:
js901 affects unc-104 function in anterograde synaptic vesicle transport. Based on column 8 WBVar02141295 ->js901, column 3 unc-104, column 5 GO:00048490
js415 affects sam-4 function in the regulation of anterograde synaptic vesicle transport. Based on column 8 WBVar02125688 -> js415, column 3 sam-4, column 5 GO:1903744 -> positive regulation of anterograde synaptic vesicle transport -> Replace "positive" with "the" -> the regulation of anterograde synaptic vesicle transport
- Rule 5: Italicize <variation> public name and column 3 gene
- Rule 6: If there are two variations listed in column 8, make a summary for each variation each using the GO value in column 5 of the line
- Rule 7: If the genes and alleles are the same in each line, concatenate GO:IDs, comma separate or join with “and”
*Example: *nj21 affects maco-1 function in chemotaxis and neuronal signal transduction *nj34 affects maco-1 function in chemotaxis and neuronal signal transduction
Building Phenotype Observed summary sentences using phenotype_association file
Template for Phenotype observed sentences
<Variation> results in (defects, alterations) in <phenotype(s)>.
Ex: "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. In addition, e1368 animals have extended life spans. "
Source files Phenotype Observed data
- phenotype association file ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_association.WS251.wb
- phenotype ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest release)
- obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation
Source 1 phenotype association file:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 WB WBGene00000898 daf-2 WBPhenotype:0001682 WB:WBVar00143949 IMP WB:WBPerson261 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 NOT WBPhenotype:0001688 WB:WBVar00143949 IMP WB:WBPerson261 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000190 WB_REF:WBPaper00002149 IMP WB:WBVar00088561 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 NOT WBPhenotype:0001660 WB_REF:WBPaper00006052 IMP WB:WBVar00088561 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000136 WB_REF:WBPaper00046188 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000631 WB_REF:WBPaper00036280 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000637 WB_REF:WBPaper00038179 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0001184 WB_REF:WBPaper00038379 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0001351 WB_REF:WBPaper00038379 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0001861 WB_REF:WBPaper00041295 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB
Rules for phenotype sentence construction using postgres tables
Rule 1: For lines that does not contain a value in column 4,
- extract variation(column 6 or 8),
- phenotype (column 5)
- paper(column 6)
- ex. "WB:WBVar00143947" "WBPhenotype:0001861" "WBPaper00041295"
- Map WBVariationID to Variation public_name using obo_name_variation
- Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo
Rule 2: When more than one variation exists in a line create a new line and use only one variation, with same phenotype, NOT(if exists), and paper as original line
Rule 3: Pool all phenotypes for a given variation, comma separate
Rule 4: If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s)
Building Phenotype Observed summary sentences using phenotype_association file
Template for Phenotype observed sentences
<Variation> results in (defects, alterations) in <phenotype(s)>.
Ex: "e1368 effects embryonic and larval development,
formation of the developmentally arrested dauer larval stage (diapause), adult
longevity, fat storage, salt chemotaxis learning, stress resistance, and
response to high temperature. In addition, mutants have extended life spans. "
Source files Phenotype Observed data
Source 1 postgres app tables:
app_term app_variation app_paper
- phenotype ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest release)
- obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation
Rules for phenotype sentence construction
Rule 1:
- extract variation - app_variation
- phenotype - app_term
- paper - app_paper
- ex. "WB:WBVar00143947" "WBPhenotype:0001861" "WBPaper00041295"
- Map WBVariationID to Variation public_name using obo_name_variation
- Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo
Rule 2: When more than one variation exists in a line create a new line and use only one variation, with same phenotype, NOT(if exists), and paper as original line
Rule 3: Pool all phenotypes for a given variation, comma separate
Rule 4: If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s)
Rule 5: Remove 'variant' from public names that have them
Rules for specific phenotype terms
Rule 1: For all terms that contain 'variant' remove 'variant' from public names that have them
Rule 2: For the following terms:
- WBPhenotype:0000061 - extended life span
- WBPhenotype:0001171 - shortened life span
- add an "s" to the end of the term public name
- use the phrasing "In addition, mutants have extended life spans."
- WBPhenotype:0001838 - drug induced gene expression variant
- WBPhenotype:0001871 - drug induced life span variant
- WBPhenotype:0001872 - drug induced locomotion variant
- change "induced" to "influenced"
- Terms that end in "early emb"
- replace "early emb" in the term with "in the early embryo"
- for term WBPhenotype:0001185 "embryonic developmental delay early emb", remove "embryonic"
- for term WBPhenotype:0001186 "embryo delayed at pronuclear contact early emb", remove the first term "embryo"
Building Phenotype Attribute summary sentences
Template for Phenotype Attribute summary sentences
<variation> is <app attribute>, <app attribute> <app_term>
- Ex. "s1019 is cold-sensitive, maternal effect mid larval lethal;"
<variation> is <app attribute> <app_term> at <app_heat_temp> OR <variation> is <app attribute> <app term> at <
- Ex. "e1368 is temperature sensitive dauer constitutive at 22.5 deg C;"
<variation> is <app attribute> for all phenotypes at <app_heat_degree> OR <variation> is <app attribute> for all phenotypes at <app_cold_degree>
- Ex. "oj21 is temperature sensitive for all phenotypes at 25 deg C; "
<variation> is <app_mat_effect> <app_term>
- Ex. "oj21 is maternal effect embryonic lethal;"
Source for Phenotype Attribute sentence
postgres app tables
Rules for Phenotype Attribute summary sentences
Rule 1: when there are more than one phentoype attribute sentences, use the generic "animals" instead of repeating the allele name
- Ex "oj21 is temperature sensitive for all phenotypes at 25 deg C; oj21 is maternal effect embryonic lethal; animals are 100% sterile at 25 degrees C;"
Building Phenotype NOT Observed summary sentences
Template for Phenotype NOT observed sentences
<Allele> does not show (defects, alterations) in <NOT phenotype(s)>.
- Ex. "e1368 animals do not show any defects in acetylcholine esterase activity, carbon dioxide avoidance, diacetyl chemotaxis, and DMPP response."
Source files Phenotype Observed data
- phenotype association file ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_association.WS251.wb
- phenotype ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest release)
- obo_name_variation tazendra home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/obo_name_variation
Source 1 phenotype association file:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 WB WBGene00000898 daf-2 WBPhenotype:0001682 WB:WBVar00143949 IMP WB:WBPerson261 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 NOT WBPhenotype:0001688 WB:WBVar00143949 IMP WB:WBPerson261 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000190 WB_REF:WBPaper00002149 IMP WB:WBVar00088561 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 NOT WBPhenotype:0001660 WB_REF:WBPaper00006052 IMP WB:WBVar00088561 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000136 WB_REF:WBPaper00046188 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000631 WB_REF:WBPaper00036280 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB WB WBGene00000898 daf-2 WBPhenotype:0000637 WB_REF:WBPaper00038179 IMP WB:WBVar00143947 P Y55D5A.5 gene taxon:6239 20151027 WB
Rules for phenotype sentence construction
Rule 1: For each line that contains (NOT) value in column 4, extract
- variation(column 6 or 8),
- phenotype (column 5)
- paper(column 6)
- NOT(column 4)
- ex. "WB:WBVar00143947" "NOT" "WBPhenotype:0000114" "WBPaper00039871"
- Map WBVariationID to Variation public_name using obo_name_variation
- Map WBPhenotype to Phenotype name using phenotype_ontology.WS251.obo
Rule 2: When more than one variation exists in a line create a new line and use only one variation, with same phenotype, and paper as original line
Rule 3: Pool all NOT phenotype for a given variation, separate
Rule 4: If a Phenotype term in the list is a parent of (is_a or part_of parent) another Phenotype term in the list, keep the most granular child term and ignore the parent term(s)
Rule 5: Remove 'variant' from public names that have them
Building Disease Orthology summary sentences
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
Examples for concise descriptions for variations of different types
- Classic alleles
notes: can add: mutagen, history of isolation
- Alleles with molecular data
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 6 coding 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.
- Alleles with only genetic data
- Other variation types
- Engineered alleles
- Integrated transgenes
other categories of alleles
- Most published alleles
- Alleles with most phenotypes
- Alleles of genes with concise descriptions (see concise description wiki to find these)
Prioritizing variations for automated descriptions
- 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
Orthology/ Conserved 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 Sentences to make: *Molecular sentence 2: "qx18 encodes a C to T transition, T67M which affects the phosphate/Mg2+ binding domain PM3" *Orthology sentence: "The phosphate/Mg2+ binding domain PM3 is conserved in all members of the Ras GTPase superfamily"
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 . Sentence to make: *Molecular sentence 2: "n1619 encodes a L131P substitution in the c-abl SH3 domain"
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 . Sentence to make: *Molecular sentence 2: "n1950 encodes a G169E change in the BH3 binding pocket of CED-9"
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-dependent MAPK activation.” Sentence to make: *Molecular sentence 2: "sy262 encodes a G33R mutation in the Rac GEF Dbl domain and is equivalent to a C282R change in the human hSOS1." *Orthology sentence: "The sy262 G33R mutation is equivalent to a C282R change in the human hSOS1."
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] Sentence to make: *Molecular sentence 2: "ad1302 encodes a Val to Glu change." *Orthology sentence: "ad1302 affects a region that is conserved in GluCl subunits as well as in rat glycine and GABA type A-channel subunits."
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-of function 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] Sentence to make: *Molecular sentence 2: "q624 encodes a D to E change in the catenin binding domain" *Orthology sentence: "q624 affects a conserved amino acid in the HMG-box DNA binding domain specifically in TCF/LEF-1 type HMG proteins"
on Textpresso-dev
The directory structure should be something like
- descriptions/ (descriptions and stats per release)
- source_files/ (common input files, including variation. gene, obos, etc)
- molecular/ (phrases generated from molecular info input)
- process/ (phrases generated from go input)
- phenotype/ (phrases generated from phenotype input)
on postgres
- The latest dump:
- Variation concise description pipeline:
- Scripts:
- Output location:
Order of sentences
- Molecular sentence 1
- Molecular sentence 2
- Disease/Orthology
- Process
- Phenotype observed
- Phenotype attribute
- Phenotype NOT observed
Postgres sources
Source files for phenotype attribute data for variation concise description *OA (app) tables: **app_variation **app_term app_paper, app_easescore, app_mmateff, app_hmateff, app_molecule, app_anatomy, app_lifestage, app_penetrance, app_mat_effect, app_temperature, app_cold_degree, app_heat_degree, app+pat_effect app_haplo, app_cold_sens, app_heat_sens <pre> need to adapt for variation concise description **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'.
Preliminary results
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 | Last Updated | Date when the descriptions were last generated |
2014-09-11 | Required | vcd_lastupdate |
9 | pgid | pgid | 1149 (Postgres will generate) |
Required |
Tab-delimited file for OA insert
(for gene concise desc, for reference)
- 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
Use same structure as for gene concise descriptions (which follows)
- 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
Scripts for automated concise descriptions (for reference)
- /home/acedb/ranjana/concise_testing/populate_automated_concise_descriptions.pl -> /home/postgres/work/pgpopulation/concise_description/20140909_automated_concise/populate_automated_concise_descriptions.pl
which look at
- http://textpresso-dev.caltech.edu/concise_descriptions/production_release.txt for release number
- http://textpresso-dev.caltech.edu/concise_descriptions/species.txt for the different species
For testing on Mangolassi
Dumping to .ace
Tracking progress
Generate a report for numbers and place on Textpresso-dev
- Report for each upload:
- Total number of automated variation descriptions =
- Number of automated descriptions with molecular details =
- Number of automated descriptions with gene function/GO information =
- Number of automated descriptions with phenotype information =
- Number of automated descriptions with human disease reference =
Changes/Updates for each release
Issues to address
Automated descriptions software
Follow gene concise description pipeline Documentation for workflow and scripts
- 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