Difference between revisions of "Source and maintenance of non-WBGene info"
From WormBaseWiki
Jump to navigationJump to searchm |
m |
||
Line 15: | Line 15: | ||
|- | |- | ||
|Variation | |Variation | ||
− | | | + | |obo_name_variation<br>obo_data_variation |
|yes | |yes | ||
|yes | |yes | ||
Line 26: | Line 26: | ||
|no | |no | ||
|no | |no | ||
− | | | + | | |
|- | |- | ||
|Variation public_name | |Variation public_name | ||
− | | | + | |obo_name_variation<br>obo_data_variation |
|no | |no | ||
|yes | |yes | ||
Line 43: | Line 43: | ||
|- | |- | ||
|Variation- Gene | |Variation- Gene | ||
− | | | + | |obo_data_variation |
|no | |no | ||
|yes | |yes | ||
Line 57: | Line 57: | ||
|- | |- | ||
|Variation -Reference | |Variation -Reference | ||
− | | | + | |obo_data_variation |
|no | |no | ||
|yes | |yes | ||
Line 71: | Line 71: | ||
|- | |- | ||
|Variation -Method | |Variation -Method | ||
+ | |obo_data_variation | ||
+ | |no | ||
+ | |yes | ||
+ | |yes | ||
+ | |no | ||
| | | | ||
| | | | ||
Line 77: | Line 82: | ||
| | | | ||
| | | | ||
− | | | + | |Only take these Method "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 |
|no | |no | ||
|yes | |yes | ||
Line 99: | Line 99: | ||
|- | |- | ||
|Rearrangement | |Rearrangement | ||
− | | | + | |obo_name_rearrangement<br>obo_data_rearrangement |
|no | |no | ||
|yes | |yes | ||
Line 113: | Line 113: | ||
|- | |- | ||
|Rearrangement -map | |Rearrangement -map | ||
− | | | + | |obo_data_rearrangement |
|no | |no | ||
|yes | |yes | ||
Line 127: | Line 127: | ||
|- | |- | ||
|gene_inside | |gene_inside | ||
− | | | + | |obo_data_rearrangement |
|no | |no | ||
|yes | |yes | ||
Line 141: | Line 141: | ||
|- | |- | ||
|gene_outside | |gene_outside | ||
− | | | + | |obo_data_rearrangement |
|no | |no | ||
|yes | |yes | ||
Line 155: | Line 155: | ||
|- | |- | ||
|Strain | |Strain | ||
− | | | + | |obo_name_strain<br>obo_data_strain |
|no | |no | ||
|yes | |yes | ||
Line 169: | Line 169: | ||
|- | |- | ||
|Strain -genotype | |Strain -genotype | ||
− | | | + | |obo_data_strain |
|no | |no | ||
|yes | |yes | ||
Line 183: | Line 183: | ||
|- | |- | ||
|Strain- location | |Strain- location | ||
− | | | + | |obo_data_strain |
|no | |no | ||
|yes | |yes | ||
Line 197: | Line 197: | ||
|- | |- | ||
|Clone | |Clone | ||
− | | | + | |obo_name_clone<br>obo_data_clone |
|no | |no | ||
|yes | |yes | ||
Line 211: | Line 211: | ||
|- | |- | ||
|Clone -Type | |Clone -Type | ||
− | | | + | |Not sure you need a table for this. All clones that populate the clone tables will be of one type = PLASMID |
|no | |no | ||
|yes | |yes | ||
Line 225: | Line 225: | ||
|- | |- | ||
|Clone -Transgene | |Clone -Transgene | ||
− | | | + | |obo_data_clone |
|no | |no | ||
|yes | |yes | ||
Line 236: | Line 236: | ||
|no | |no | ||
|no | |no | ||
− | | | + | |I don't think there is any data in this tag in the ftp cloness.ace |
|- | |- | ||
|Clone -strain | |Clone -strain | ||
+ | |obo_data_clone | ||
+ | |no | ||
+ | |yes | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
| | | | ||
+ | |- | ||
+ | |Clone -general_remark | ||
+ | |obo_data_clone | ||
|no | |no | ||
|yes | |yes | ||
Line 252: | Line 266: | ||
| | | | ||
|- | |- | ||
− | |Clone - | + | |Clone -location |
+ | |obo_data_clone | ||
+ | |no | ||
+ | |yes | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
| | | | ||
+ | |- | ||
+ | |Clone -accession_number | ||
+ | |obo_data_clone | ||
|no | |no | ||
|yes | |yes | ||
Line 266: | Line 294: | ||
| | | | ||
|- | |- | ||
− | | | + | |Laboratory |
+ | |obo_name_laboratory<br>obo_data_laboratory | ||
+ | |no | ||
+ | |yes | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
| | | | ||
+ | |- | ||
+ | |Laboratory -Representative | ||
+ | |obo_name_laboratory<br>obo_data_laboratory | ||
|no | |no | ||
|yes | |yes | ||
Line 280: | Line 322: | ||
| | | | ||
|- | |- | ||
− | | | + | |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 | |no | ||
|yes | |yes | ||
Line 294: | Line 350: | ||
| | | | ||
|- | |- | ||
− | | | + | |Laboratory - strain_designation |
+ | |obo_data_laboratory | ||
+ | |no | ||
+ | |yes | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
+ | |yes | ||
+ | |no | ||
+ | |no | ||
+ | |no | ||
| | | | ||
+ | |- | ||
+ | |Laboratory -Mail | ||
+ | |obo_data_laboratory | ||
|no | |no | ||
|yes | |yes |
Revision as of 20:42, 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 | no | no | yes | yes | no | no | no | no | |
Variation public_name | obo_name_variation obo_data_variation |
no | yes | yes | no | no | yes | yes | no | for Variation first pass | For Variation lexicon | In multiple OAs |
Variation- Gene | obo_data_variation | no | yes | yes | no | no | no | yes | no | no | no | |
Variation -Reference | obo_data_variation | no | yes | yes | no | no | no | yes | no | yes? | no | |
Variation -Method | obo_data_variation | no | yes | yes | no | Only take these Method "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 | no | yes | yes | no | no | no | yes | ? | 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 | no | no | no | |
gene_outside | obo_data_rearrangement | no | yes | yes | no | no | no | yes | no | no | no | |
Strain | obo_name_strain obo_data_strain |
no | yes | yes | no | no | no | 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 | no | yes | no | no | no | |
Laboratory -Representative | obo_name_laboratory obo_data_laboratory |
no | yes | yes | no | no | no | 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 | no | no | |
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 |