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

• 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

NB:

• western^t " this tag was used 19 times and has always text
• Antibody^t " this tag was used 462 times and has always text

• 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

Expr_pattern model

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?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern CDS ?CDS XREF Expr_pattern // for coding genes Sequence ?Sequence XREF Expr_pattern // for clones??? Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb] Clone ?Clone XREF Expr_pattern Protein ?Protein XREF Expr_pattern

                               Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]

Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2] Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier Cell_group ?Cell_group XREF Expr_pattern #Qualifier Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition

               Subcellular_localization ?Text

Type Reporter_gene ?Text In_situ Text Antibody ?Text Northern Text // Wen [krb 030425]

                       Western Text  // Wen 
                       RT_PCR Text   // Wen

Localizome ?Text //added by Wen Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome Pattern ?Text Picture ?Picture XREF Expr_pattern MovieURL Text //Added by wen for link to movie URLs. Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video

               Remark ?Text #Evidence
               Experiment	Laboratory ?Laboratory

Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern

               Transgene ?Transgene XREF Expr_pattern

Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining

                                                         // added [031120 krb]

Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]

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