Specifications for a Community Annotation Form

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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
Left heading Box type Guide-lines to right of field
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 gene Auto-complete ontology drop-down Start typing in a gene and then choose from the drop-down menu.
Choose a species Auto-complete ontology drop-down Start typing in the name of a species and then choose from the drop-down menu.
WormBase provided description Pre-filled text box with either concise or automated description, non-editable If concise description exists wording is: Update/edit this description in the box below. If automated description: Update/edit this description in the box below. This description was generated by scripts based on homology/orthology data and Gene Ontology annotations in WormBase.
If neither a manual or automated description exists, the form will return a "This gene does not yet have a description" and the 'New gene description' box appears.
New gene description Free text box Copy the description from the box above and paste into this box for editing, or write a new description. Guidelines on what to include are here http://wiki.wormbase.org/index.php/How_WormBase_writes_a_concise_description
Enter a single PMID paper reference per line (e.g., PMID:4366476). Box for entering PMIDs Check that the PMIDs you entered are correct by checking their details below. Please note that WormBase will not accept meeting abstracts, gazette articles or personal communications as references.

Adding User submitted gene descriptions to the workflow

  • Each user submission via the form will create a new row in the OA, note if the same User hits 'Submit' multiple times, multiple rows will be created
  • There will be a 'User submission' field in the OA, which is a toggle
  • There needs to always be a 'Curator' associated with a description, this relates to the pgids
  • User submissions will be toggled to 'No dump' by default
  • User submissions will have to be reviewed by a curator
  • For querying purposes, there will exist a 'Reviewed' and 'Not-reviewed' option, preferably a drop-down and not a toggle
  • Multiple user submissions will have to be consolidated into one concise description, the 'master'
  • References will have to be transferred from User submissions to the 'master'
  • There should only be one 'master' concise description
  • If there is only one gene description, will have to duplicate this to a 'master', remove the 'user submission' flag from the master
  • Only the master concise description will be dumped


Mapping fields in the form to fields in the OA

Name of field in Form Name of field in OA OA field type Postgres table name Ontology_table Required?
Enter your name WBPerson Single ontology con_person WBPerson ontology Yes
WBPerson ID WBPerson Single ontology con_person WBPerson ontology Yes
Choose a species Species Single ontology con_species Species ontology Yes
WormBase provided description Concise or Automated description Text box con_desctext N/A Yes
Contributed by WBPerson Single ontology con_person WBPerson ontology Yes
E-mail address User e-mail WBPerson ontology? Yes
New gene description Description Type:Concise_description Drop-down con_desctype N/A Yes
New gene description Description Text Text-box con_desctext N/A No
Enter the PMID of a paper reference Reference Multi-ontology con_paper WBPaper ontology Yes
(For PMIDs with no WBPaper) Unmapped PMIDs No
(No field) Curator drop-down con_curator Yes
(No field) Curator history clicking brings up term info con_curhistory Yes
(No field) Not_reviewed toggle Yes
(No field) User_submission toggle Yes
(No field) Review status drop-down:Needs review, Reviewed No
(No field) Master description Yes,unless not reviewed yet

Pending requests to the form

  • Can the autocomplete gene list be set by the species entered, i.e. if a user selects C. elegans from the species list can the resulting gene list be restricted to C. elegans genes? (Kimberly)
  • Should we accept doi's for paper identifiers? If an entered paper identifier doesn't map to a WBPaper ID it shows in the email that we get, right? (Kimberly)
  • Ranjana: For now the Preview page could be as simple as:

Thank-you for your submission!  You submitted the following:

Name: Ranjana Kishore (WBPerson324)
E-mail address: xyz@upenn.edu
Species: Caenorhabditis elegans
Gene: abc-1 (WBGene00000011)
New gene description: let-526 encodes a homolog of a component of the SWI/SNF complex; the let-526(h185) mutation results in early larval lethality.
Paper references: PMID:4366476, PMID:4789342
Contributed by: Hitoshi Sawa (WBPerson552), Masahiro Uchida (WBPerson4638), Ranjana Kishore (WBPerson324)
Date: 2015-02-19

If you would like to edit or correct any entry, please do so in the form below.

Changes to the form based on User testing

  • 'Save' button: User should get an e-mail with the link, instead of being taken to a page with a link that they have to copy and save for later.

E-mail could look like:


Subject: Link for WormBase Community Gene Description form

Please continue your submission through the WormBase Community Gene Description form, for <gene>, from <species>, started on <date>, with this link:

Thank-you
WormBase

  • 'Contributed by': Change to 'Previously contributed by'
  • Add right-hand side guideline: to 'Previously contributed by' to say 'People who have previously written or edited this gene description'
  • Have 'Preview' a static page, not editable, and a button to go back to the live form (will leave this out for now, if we get more users saying this, we can revisit).
  • Have all form instructions in bigger and bold font and have appreciable space around them: eg., All fields are required, You failed to enter data in mandatory fields...,