Expression Pattern

Expression Pattern

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

Laboratory (22x) 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 - bigtaxt, 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

Tab2

• Laboratory - text
• Protein_description - text
• Author - Multiontology on people
• Date - text

• Remark - bigtext

• URL_Accession - text
• Person - Multiontology on people
• Person_text - free text. The person text was created for cases when we want to acknowledge people that are not WBPersons. Note on the .ace file for Person and Person_name: join all <pic_person> objects's starndard names with commas, then comma, then <pic_persontext> text. If there's no <pic_persontext>: join all person objects's standard names with commas, except for the last one, which is joined by "<comma> and ". Daniela remember for curation when you enter a text in the person text you should do the following: If it is a single entity in the text write e.g. "and Paul Sternberg's lab" if there are multiple entities e.g. summer student 1 (non WBPerson), summer student 2 (non WBPerson), and summer student 3 (non WBPerson) write "John Smith, George Brown, and Mike Lee". It is constructed in this way otherwise the syntax would have been too complicated

• Curator - Multiontology on people
• No dump - Toggle