Specifications for a Community Annotation Form

Description of fields

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/community_gene_description.cgi

1. Enter your first name.

Free text box; required

2. Enter your last name

Free text box; required

3. Enter a contact E-mail address

Free text box; required

4. Choose a species.

Autocomplete, Drop-down with predetermined values, if not found, free text is allowed. The preferred order is (note that Homo sapiens has been taken out):

• Caenorhabditis elegans
• Caenorhabditis briggsae
• Pristionchus pacificus
• Brugia malayi
• Caenorhabditis brenneri
• Caenorhabditis japonica
• Caenorhabditis remanei
• Caenorhabditis sp. 3
• Panagrellus redivivus
• Cruznema tripartitum

5. Choose a gene gin_locus gin_synonyms gin_seqname gin_wbgene this is the priority of how genes get autocompleted

J: If what is typed does not match, it stays as free-text

6.Write a concise description for the gene you've chosen.

Concise description: A big box for free-text, similar to the 'Description Text' box in the Concise Description OA.

7. Reference Box allowing PMID only.

Also, once PMID is entered, form pulls up Paper information, meaning title etc etc, similar to what P2GO does; Kimberly will talk to JC about it.

Here is the information we got from Tony on how this feature works in Protein2GO:

> We use the Europe PubMed Central web services for doing the lookup and validation - you can find details of all their available services at http://europepmc.org/RestfulWebService

> Here's an example of the kind of request that we make in order to do the validation:

> www.ebi.ac.uk/europepmc/webservices/rest/search/format=json&query=src:medANDext_id:16043488

Mock-up of form with field titles and guidelines

1. Enter your first name.

2. Enter your last name.

3. Enter a contact E-mail address.

4. Choose a species.

Start typing in a species name. The form will auto-complete the text and present a list of species below the box. Click anywhere on the species you want to enter that species name in the box. If you cannot find the species in the drop-down, please enter it manually.

5. Choose a gene

Enter a gene name (e.g., abc-1). Sequence names (e.g., AC3.4) and WBGene IDs (e.g., WBGene00000011) are allowed. If the gene you begin typing matches a valid WormBase gene name, then a list of possible matches will be presented below the box. To select a gene, click anywhere on the name of that gene and it will be entered into the box. If you cannot find the gene in the drop-down, please enter it manually.

6. Write a concise description for the gene you've chosen.

Please see guidelines on writing a concise description: http://wiki.wormbase.org/index.php/How_WormBase_writes_a_concise_description

7. Enter the PMID of a published paper reference.

Please enter a single PMID identifier per line (e.g., PMID:4366476). Please note that WormBase will not accept meeting abstracts, gazette articles or personal communications as references.

Suggested changes to Form

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/community_gene_description.cgi

User Interface

• Will look better if the right edges of the boxes for the fields are lined up.
• Make the guidelines font bigger, if there is more space between the boxes, the font could get bigger. I think its okay for the form to grow vertically. I agree; I think we want to make sure the instructions are big enough so people will/can read them more easily.
• When text is entered in the concise description box on Firefox, it looks squished by the 'Choose a gene' box on top. In the Safari browser, there is actually space between the two boxes (and in between other boxes).
• Would be nice to have a 'Go back to form' button from the submitted page.
• Gene name auto-complete needs to be case-insensitive. Typing in Ppa-lin-17 doesn't auto-complete but typing in ppa-lin-17 does. Since Ppa-lin-17 is actually the official gene name, it should also be recognized by the auto-complete function.
• If a PMID doesn't map to an existing WBPaper ID, it would nice to be alerted in the email so we can create the new WBPaper object.
• We may need to have more specific instructions on how to enter PMIDs. If I enter references in the format below (the line between the two is from wiki, on the form the second reference is on the next successive line, i.e., there is no line separating the two):

PMID:23721876

23555279

then the two IDs are getting concatenated and the resulting ID is not valid.

• For PMID:23721876, there is a special character in the title that is being replaced by questions marks inside of black diamonds that seem to be increase in number if I leave the page and come back.
• If a user deletes a reference from the PMID list, it should also delete from the title list and not be included as evidence for the description.

Adapting the form for community editing of Automated descriptions

Specifications of form

Right heading	Box type	Guide-lines to left of box
Enter your first name	Free text box	(No wording)
Enter your last name	Free text box	(No wording)
E-mail address	Free text box	(No wording)
Choose a species	Auto-complete drop-down	Start typing in the name of a species, and then choose from the drop-down menu.
WormBase provided automated description	Pre-filled text box with automated description, non-editable	This description was generated by scripts based on homology/orthology data and Gene Ontology annotations in WormBase.
Edit WormBase provided automated description	Free text box, expands as the description gets bigger?	Copy the automated description in the box above and paste into this box for editing.
References: Enter a single PMID paper reference per line (e.g., PMID:4366476).	Box for entering PMIDs	Please note that WormBase will not accept meeting abstracts, gazette articles or personal communications as references.