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, yes/no etc. 

OA interface

• 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.
• Life_stage - multiontology like in the phenotype OA and picture OA
• Type - multidropdown select from: Antibody, Reporter_gene, In_situ, RT_PCR, Northern, Western

• Contact - Multiontology on people. N.B. when you have more than one Contact be aware on how to name the folder that stores pictures. As a general rule the folder should always be called after the first person inserted.
• Description - Figure legend (bigtext)
• Source - Multiontology from file picture_source on Tazendra (acedb@tazendra.caltech.edu:/home/acedb/draciti/)
• Cropped_From - Multiontology on source then WBPicture name/ID. Show on Term Info name/ID, source, reference.
• Expr_pattern - source file in Tazendra: /home/acedb/draciti/ExprWS221.ace. In term info we'd like to see Gene, Pattern, Reference, Reporter_gene, Life_stage Anatomy_term, GO_term. Autocomplete just on Expr_pattern ID.
• 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