Expression Pattern

Expression Pattern

Tags currently used in Expr_pattern objects (based on WS221):

Laboratory Expr_pattern Pattern Life_stage Gene Antibody Subcellular_localization GO_term Western Transgene Protein_description In_Situ Author Anatomy_term Reporter_gene Picture Date Reference Expressed_in Antibody_info Protein Northern Clone Cell RT_PCR Strain Remark MovieURL Pseudogene Curated_by Sequence

Types of fields Juancarlos can implement:

   * text : text
   * bigtext : text box expanded
   * dropdown : few values
   * ontology : controlled vocabulary 
   * multiontology / multidropdown : allows multiple values
   * toggle : on / off

OA interface

Tab1

• Pgdbid -- postgres database ID, generates automatically upon entry.
• Expr_pattern -- same as in interaction
  • no Expr_pattern ID is generated by clicking on 'new'. when 'duplicate', the ID from old entry will be in the field, but need to be deleted in order to get an new ID.
  • Expr_pattern ID should be assigned by cronjob daily at 4 am. start assigning with Expr10001
• Reference -- ontology on paper WBPaperID - Daniela add wish list for term info
• Gene -- ontology on genes WBGeneID - show WBID, locus, and synonym in term info as in GO OA
• Anatomy term - multiontology. Controlled vocabulary found here: http://brebiou.cshl.edu/viewcvs/*checkout*/Wao/WBbt.obo (same as in Picture OA)
• GO_term - multiontology of GO_Term like gop_goid.
• Subcellular_localization - bigtext, details on subcellular localization.
• Life_stage - multiontology like in the phenotype OA and picture OA
• Type - Wen suggested multidropdown select from: Antibody, Reporter_gene, In_situ, RT_PCR, Northern, Western but this is not possible because we have text associated to those values

NB:

• Antibody^t " this tag was used 462 times and has text associated -> not possible just to toggle
• Reporter_gene^t " this tag was used 7273 times and has been used twice for the same object!
• In_situ^t " this tag was used 434 times and has always text -> not possible just to toggle
• RT_PCR^t " this tag was used 165 times has text associated -> not possible just to toggle
• Northern^t " this tag was used 347 times and has text or just Northern label -> not possible just to toggle
• Western^t " this tag was used 19 times and has always text -> not possible just to toggle

• Antibody_info -- ontology on antibodies? Wen, in the Antibody OA there's no reference to Expr_pattern I thought this field would have been a multiontology on Antibodies.
• Reporter_gene bigtext, details on reporter gene construct
• pattern bigtext, details on tissue distribution
• remark bigtext, if any comments required
• transgene multiontology on transgenes
• Curator - Multiontology on people
• No dump - Toggle

Tab2

• Protein_description - text (30 objects)
• Clone - text (341 objects)multiontology on clones? Is there a clone obo?
• Strain - text (812 objects)Is there a strain obo?
• Cell - multiontology on anatomy terms (26 objects)-> when this is live consolidate these objects with the Anatomy_term field
• Pseudogene - text (1 object)
• Sequence - text (13 objects) F54E2 2x (clone), R05D8 2x (clone), Y38B5A (clone), "Z28375" -C "EMBL Z28375" (sequence), "Z28376" -C "EMBL Z28376" (sequence), "Z28377" -C "EMBL Z28377" (sequence), R11H6 (clone), Y40H4A (clone), U14525, C47G2 (clone), Z32673 (sequence). Wen, should we move the Clone objects to Clone?
• Laboratory - text (17 objects)
• Author - Multiontology on people
• Date - text (2617 objects)
• Curated_by - text (6228 objects)

Tags used only once that should be fixed

• Expressed_in - text 1 entry
• Protein - text 1 entry could be put in Protein_description