Difference between revisions of "Source and maintenance of non-WBGene info"

From WormBaseWiki
Jump to navigationJump to search
m
m
Line 15: Line 15:
 
|-
 
|-
 
|Variation
 
|Variation
|obo_name
+
|obo_name_variation<br>obo_data_variation
 
|yes
 
|yes
 
|yes
 
|yes
Line 26: Line 26:
 
|no
 
|no
 
|no
 
|no
|Only select variations based on Method will be sent daily.
+
|
 
|-
 
|-
 
|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 -general_remark
+
|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:
 
|
 
|
 
|-
 
|-
|Clone -location
+
|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:
 
|
 
|
 
|-
 
|-
|Clone -accession_number
+
|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:
 
|
 
|
 
|-
 
|-
|Clone -reference
+
|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