Difference between revisions of "Source and maintenance of non-WBGene info"
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|Variation | |Variation | ||
|obo_name_variation<br>obo_data_variation | |obo_name_variation<br>obo_data_variation | ||
+ | |yes | ||
|yes | |yes | ||
|yes | |yes | ||
|no | |no | ||
|no | |no | ||
+ | |yes | ||
|yes | |yes | ||
|yes | |yes | ||
|no | |no | ||
|no | |no | ||
− | | | + | |WBVariationID |
− | |||
− | |||
|- | |- | ||
|Variation public_name | |Variation public_name | ||
Line 38: | Line 38: | ||
|yes | |yes | ||
|no | |no | ||
− | | | + | |For Mary Ann's Variation first pass/SVM |
|For Variation lexicon | |For Variation lexicon | ||
|In multiple OAs | |In multiple OAs | ||
Line 50: | Line 50: | ||
|no | |no | ||
|no | |no | ||
− | |yes | + | |yes <br>Display WBGeneID and gin_locus |
|no | |no | ||
|no | |no | ||
Line 66: | Line 66: | ||
|yes | |yes | ||
|no | |no | ||
− | |yes? | + | |yes? for MA's scripts?? |
|no | |no | ||
| | | | ||
Line 73: | Line 73: | ||
|obo_data_variation | |obo_data_variation | ||
|no | |no | ||
+ | |no <br>used to query for Variation type Allele and Transposon | ||
|yes | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
|yes | |yes | ||
|no | |no | ||
− | | | + | |no |
− | | | + | |no |
− | |||
− | |||
− | |||
− | |||
|Only take these Methods<br>"Allele"<br>"Deletion_allele"<br>"Deletion_and_insertion_allele"<br>"Deletion_polymorphism<br>"Insertion_allele"<br>"Insertion_polymorhism"<br>"KO_consortium_allele"<br>"Mos_insertion"<br>"NBP_knockout_allele"<br>"NemaGENETAG_consortium_allele"<br>"Substitution_allele"<br>"Transposon_insertion" | |Only take these Methods<br>"Allele"<br>"Deletion_allele"<br>"Deletion_and_insertion_allele"<br>"Deletion_polymorphism<br>"Insertion_allele"<br>"Insertion_polymorhism"<br>"KO_consortium_allele"<br>"Mos_insertion"<br>"NBP_knockout_allele"<br>"NemaGENETAG_consortium_allele"<br>"Substitution_allele"<br>"Transposon_insertion" | ||
|- | |- | ||
− | |Status | + | |Status |
|obo_data_variation | |obo_data_variation | ||
− | | | + | |yes |
|yes | |yes | ||
|yes | |yes | ||
Line 93: | Line 93: | ||
|no | |no | ||
|yes | |yes | ||
− | | | + | |no |
|no | |no | ||
|no | |no | ||
Line 134: | Line 134: | ||
|no | |no | ||
|no | |no | ||
− | |yes | + | |yes <br>display gin_locus (do not need WBGeneID) |
|no | |no | ||
|no | |no | ||
Line 148: | Line 148: | ||
|no | |no | ||
|no | |no | ||
− | |yes | + | |yes <br>display gin_locus (do not need WBGeneID) |
|no | |no | ||
|no | |no | ||
Line 161: | Line 161: | ||
|no | |no | ||
|no | |no | ||
− | | | + | |yes |
|yes | |yes | ||
|no | |no | ||
Line 301: | Line 301: | ||
|no | |no | ||
|no | |no | ||
− | | | + | |yes |
|yes | |yes | ||
|no | |no | ||
Line 315: | Line 315: | ||
|no | |no | ||
|no | |no | ||
− | | | + | |yes |
|yes | |yes | ||
|no | |no | ||
Line 346: | Line 346: | ||
|yes | |yes | ||
|no | |no | ||
− | | | + | |yes MA's script |
− | | | + | |yes? use for text markup regex? |
| | | | ||
|- | |- |
Revision as of 21:01, 27 September 2013
AceDB tag | Postgres table | Current - Nameserver nightly dump | Current - WS bimonthly release | Future - Geneace nightly dump | Future - WS bimonthly release | Use - Paper or meeting abstract gene connection | Use - OA data type curation | Use - OA term info | Use - Dumping scripts | Use -Text mining/SVM | Use - Updating GSA Lexicon | Comment |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Variation | obo_name_variation obo_data_variation |
yes | yes | yes | no | no | yes | yes | yes | no | no | WBVariationID |
Variation public_name | obo_name_variation obo_data_variation |
no | yes | yes | no | no | yes | yes | no | For Mary Ann's Variation first pass/SVM | For Variation lexicon | In multiple OAs |
Variation- Gene | obo_data_variation | no | yes | yes | no | no | no | yes Display WBGeneID and gin_locus |
no | no | no | |
Variation -Reference | obo_data_variation | no | yes | yes | no | no | no | yes | no | yes? for MA's scripts?? | no | |
Variation -Method | obo_data_variation | no | no used to query for Variation type Allele and Transposon |
yes | no | no | no | yes | no | no | no | Only take these Methods "Allele" "Deletion_allele" "Deletion_and_insertion_allele" "Deletion_polymorphism "Insertion_allele" "Insertion_polymorhism" "KO_consortium_allele" "Mos_insertion" "NBP_knockout_allele" "NemaGENETAG_consortium_allele" "Substitution_allele" "Transposon_insertion" |
Status | obo_data_variation | yes | yes | yes | no | no | no | yes | no | no | no | |
Rearrangement | obo_name_rearrangement obo_data_rearrangement |
no | yes | yes | no | no | yes | yes | no | no | yes | |
Rearrangement -map | obo_data_rearrangement | no | yes | yes | no | no | no | yes | no | no | no | |
gene_inside | obo_data_rearrangement | no | yes | yes | no | no | no | yes display gin_locus (do not need WBGeneID) |
no | no | no | |
gene_outside | obo_data_rearrangement | no | yes | yes | no | no | no | yes display gin_locus (do not need WBGeneID) |
no | no | no | |
Strain | obo_name_strain obo_data_strain |
no | yes | yes | no | no | yes | yes | no | no | yes | |
Strain -genotype | obo_data_strain | no | yes | yes | no | no | no | yes | no | no | no | |
Strain- location | obo_data_strain | no | yes | yes | no | no | no | yes | no | no | no | |
Clone | obo_name_clone obo_data_clone |
no | yes | yes | no | no | yes (expr_pattern) | yes | no? | no | yes | |
Clone -Type | Not sure you need a table for this. All clones that populate the clone tables will be of one type = PLASMID | no | yes | yes | no | no | no | yes | no | no | no | |
Clone -Transgene | obo_data_clone | no | yes | yes | no | no | no | yes | no | no | no | I don't think there is any data in this tag in the ftp cloness.ace |
Clone -strain | obo_data_clone | no | yes | yes | no | no | no | yes | no | no | no | |
Clone -general_remark | obo_data_clone | no | yes | yes | no | no | no | yes | no | no | no | |
Clone -location | obo_data_clone | no | yes | yes | no | no | no | yes | no | no | no | |
Clone -accession_number | obo_data_clone | no | yes | yes | no | no | no | yes | no | no | no | |
Laboratory | obo_name_laboratory obo_data_laboratory |
no | yes | yes | no | no | yes | yes | no | no | no | |
Laboratory -Representative | obo_name_laboratory obo_data_laboratory |
no | yes | yes | no | no | yes | yes | no | no | no | |
Laboratory -Registered_lab_members | obo_data_laboratory - actually I don't know if this needs to be displayed in the term info | no | yes | yes | no | no | no | yes | no | no | no | |
Laboratory - allele_designation | obo_data_laboratory | no | yes | yes | no | no | no | yes | no | yes MA's script | yes? use for text markup regex? | |
Laboratory - strain_designation | obo_data_laboratory | no | yes | yes | no | no | no | yes | no | no | no | |
Laboratory -Mail | obo_data_laboratory | no | yes | yes | no | no | no | yes | no | no | no | |
Transgene | trp_name | no | no | no | no | no | yes | yes | yes | no | no | |
Transgene public_name | trp_publicname | no | no | no | no | no | yes | yes | yes | yes | yes | |
Transgene synonym | trp_synonym | no | no | no | no | no | yes | yes | yes | no | no | |
Transgene Summary | trp_summary | no | no | no | no | no | no | yes | yes | no | no | |
Transgene paper | trp_paper | no | no | no | no | no | no | yes | yes | yes? | no |