Gene Regulation

Types of fields Juancarlos can implement:

• text : text
• bigtext : like longtext, but makes the text box expand when you click in it so you can see everything you've written
• dropdown : few values
• ontology : controlled vocabulary (tell me where they come from)
• multiontology / multidropdown : (allows multiple values)
• toggle : on / off, yes/no etc.

Italic text== Gene_regulation OA ==

• Pgdbid - postgras database ID, entered automatically
• Reference - WBPaperID paper ontology - will you ever need to enter more than one paper? No
• Name (free text) - this gets appended to the reference to be the object name. usually a WBPaperID followed by regulated gene name, i.e.WBPaper00036472_dod-3.a
• Summary (long text) - most of time copy and paste from paper directly with curator's slight modifications do you actually want a big text box, i.e., something that expands to see all the info when you click in the box? yes, that's what I want. Then, I should say 'Big Text'

• Antibody - antibody ontology, fill the field with existing antibody, inform the curator (myself) to curate non-existing antibody objects otherwise you could have this work the way Molecule works, when you need a new antibody, you go to the Antibody OA and create, then update the ontology so you can use the new antibody right awayyes, I would like to do so. Autocomplete on antibody table -> name. in term information show -> original publication, location.

• Reporter_gene (free text) -reporter gene construct, eg. [daf-16::gfp], translational fusion is this just the transgene summary?
  yes.
• Transgene - transgene ontology, fill the field with existing transgene, (use app_tempname, or whatever gets split into for transgenes) need a way to inform transgene curator(Karen) when transgene is not existing yet

I'm not sure about what you need for these following method fields, would it work to have one field called Method and then a drop down list? or would you like to have a toggle (yes/no with default of no) for each of these values? I thought about the dropdown list for method first, then later I think, sometimes, I will need to comment in some fields. i.e. For 'RT_PCR', I will need to write ' semi-quantitative'. so a toggle with yes/no will not be enough, right?

• In_situ (toggle text) - don't have to write anything in the field, but will need method (In_situ) shown.
• Northern (toggle text) - don't have to write anything in the field, but will need method (Northern) shown.
• Western (toggle text) - don't have to write anything in the field, but will need method (Western) shown.
• RT_PCR (toggle text) - don't have to write anything in the field, but will need method (RT_PCR) shown.
• Other_method (toggle text)

• Type - drop down list with 'Change_of_localization' and 'Change_of_level'
• Regulation_level - drop down list with 'Transcriptional', 'Post_transcriptional' and 'Post_translational'
• Allele - variation ontology and a way to inform relevant curator about non-existing allele The work flow will be that you go to the NS, create the variation, update the postges variation list so the new VarID is on it (this is done by a script you will run by pressing a button), then you can enter the ID from the list.

• RNAi - need a way to inform RNAi curators (Chris and Gary) about new RNAi id requirement. there need to be a way they can come in later and fill the field I'm not sure how Juancarlos will deal with this

• Trans_regulator_gene - (multiontology on gene) I will enter gene by public/sequence name, please autocomplete with WBGeneID
• Molecule_regulator - (ontology like app_molecule) Karen's molecule ontology, and a way to inform her non-existing molecules, you will be able to create add new molecules or synonyms to molecules and update the postgres list

• Expr_pattern - (text until expr pattern OA only one value) since expr_pattern is not in postgres, I am not sure how to do this field. currently, I look up relevant expr_pattern, and copy paste into my ace file.For new expr_pattern objects, I have to wait wen to curate them first, then filled in my ace file.
• Trans_regulated_gene - I will enter gene by public/sequence name, please autocomplete with WBGeneID

• Result - dropdown of Positive_regulate, Negative_regulate, Does_not_regulate
• Anatomy_term - (multiontology app_anatomy) anatomy ontolgy
• Life_stage - (multiontology app_lifestage - check the names) life_stage ontology
• Subcellular_localization (free text) wouldn't this be a cell component GO term? , so could be the GO cell component Ontology The model was designed to enter the free text

• Remark (long text) perhaps big text? yes