Contributing Allele Phenotype Connections

From WormBaseWiki
Jump to: navigation, search

The following documentation explains the use and backend for the Allele-Phenotype form found here:

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

Watch a short video tutorial on YouTube!!!

https://www.youtube.com/watch?v=_gd87S1h3zg&feature=youtu.be


User Guide

Finding the Allele-Phenotype form

There are two main ways to reach the Allele-Phenotype form from the WormBase homepage. First, and most directly, you can click on the "Allele-Phenotype" option under the "Submit data" menu header at the top of the WormBase homepage:


WormBase homepage link to form.png


Second, the data submission summary page (accessible by clicking on the "Submit data" menu header at the top of the WormBase homepage) has a link to the form via the red "Fill out online form" button to the right of "Allele Phenotype Data Submission":


Submit data page link to form.png

Overview

The first part of the Allele-Phenotype form carries all of the fields that are required for data submission: a submitter's name and e-mail address, a publication's PubMed ID, an allele name, and a phenotype (observed or not observed):


Allele-phenotype form landing page.png


The second part of the form (made visible by clicking on the header "Optional") carries fields for optional data, pertaining to the nature of the allele with respect to the observed phenotypes indicated in the form:


Optional section expanded.png


A drop down list of options for inheritance pattern (e.g. dominant, recessive), mutation effect (e.g. loss of function, null, gain of function) and penetrance (roughly categorized as low, incomplete, high, and complete) are available. Check boxes are also available to indicate the temperature sensitivity of the allele. There is also a field for general comments for the submission. The bottom of the "Optional" section has a link to the WormBase Allele-Sequence form, by which sequence details of alleles may be reported.

Required information

The form minimally requires a submitter's name and e-mail address, a publication's PubMed ID, an allele name, and a phenotype (observed or NOT observed).

Your Name & E-mail Address

The name field has an autocomplete functionality, requiring the selection of a name from the list of registered WormBase Persons.


WBPerson autocomplete.png


If your name is not registered with WormBase, click on the green question mark to the left of the name field:


Your name field question mark.png


to open up the help text in the term information box in the upper right-hand corner of the screen and click on the "Person Update Form" link to register.


Your name field help text.png


Once a name has been selected, a term information box will appear in the upper right-hand corner of the page with additional information about this WormBase Person:


WBPerson term info.png


including a link to their WormBase Person page, as well as a link to the WBPerson publication summary page (see below). If WormBase has your e-mail address on file, it will automatically be filled into the e-mail field, otherwise you may add (or correct) your e-mail address manually.

PubMed ID

This form requires the entry of a PubMed ID (or D.O.I. if no PubMed ID exists) for the publication in which the allele-phenotype data was originally reported. PubMed IDs may be entered manually with or without the "pmid" prefix, e.g. "pmid6616618" or simply "6616618". Once an ID has been entered and recognized, a term information box will appear in the upper right-hand corner of the screen with additional information about the paper including title, journal, year, and authors list:


Paper term info.png


To assist in the look-up of PubMed IDs relevant to you, once your name has been selected a notice will appear to the right of the name field with a link to a summary of your publications and their associated PubMed IDs:


E-mail auto-populate & Name notice.png


The publication summary page consists of two tables: the top table lists papers for which WormBase data-flagging pipelines have predicted the presence of allele-phenotype data:


WBPerson publication review page top slimmer.png


and the bottom table lists papers that have not been flagged for allele-phenotype data.


WBPerson publication review page bottom.png


The top table lists the curation status of papers for which WormBase data-flagging pipelines have predicted the presence of allele-phenotype data, indicating that the paper either "Needs curation" (i.e. there are no allele-phenotype annotations for this paper), has "Curation in progress" (i.e. there is at least one annotation from a community curator using this form) or is "WormBase curated" (i.e. this paper has been curated by WormBase curators). Clicking on the "Needs curation" link will direct you to back to the Allele-Phenotype form with your name, e-mail address (if already provided), and PubMed ID of that paper pre-populated into the appopriate fields of the form:


Pre-population of PubMed ID from Needs curation link.png


In the bottom table of the publication summary page, clicking on "flag this for allele-phenotype data" will notify a WormBase curator that this paper has allele-phenotype data and should be added to the list of papers considered as having allele-phenotype data. Once clicked, you will be directed to a flagging confirmation page:


Paper flagging confirmation page.png


For papers that do not have a PubMed ID, a digital object identifier (D.O.I.) may be entered instead. In this case, the term information box will indicate that the ID is not recognized:


Unrecognized paper term info.png


but please continue with your submission, and a WormBase curator will contact you if there are any questions.

Allele Name

The allele name is required for submission of allele-phenotype data. You may enter a WormBase-recognized allele name or the name of an allele that WormBase has not yet cataloged. Start typing an allele name and suggestions will appear below the field:


Allele name autocomplete.png


Once an allele is selected from the drop down list of WormBase-recognized alleles, a term information box will appear in the upper right-hand corner of the screen with additional information about this allele:


Allele term info.png


This term information box displays links to the WormBase variation/allele page (via the "Click here..." link as well as the WBVar ID) and the WormBase gene page for the affiliated gene.

A notice will appear to the right of the field to indicate if an allele name that has been entered is not recognized by WormBase:


Unrecognized allele notice.png


If you are entering a "new" allele name, click anywhere outside the field to set the name, and continue with your submission. An allele curator will be notified and will contact you to confirm the existence of this allele.

Phenotype

By default, phenotype fields are displayed in the form for both observed and NOT observed phenotypes:


Phenotype fields default.png


The "Not Observed Phenotype" field is reserved for phenotypes that were assayed for but were not observed (were wild type) for the allele entered into the form. To enter a phenotype in either field, start typing a phenotype term or a term related to your phenotype and an auto-complete drop down list of official WormBase Phenotype Ontology (WPO) terms that match your entry will appear below the field:


Phenotype autocomplete.png


As indicated in the example image above, you may enter a three-letter code for a phenotype which will be matched to phenotype term synonyms, e.g. Let, Lvl, Vul, Muv, Pvl, Gro

Select a term from the list of WPO terms. If you cannot find your phenotype in the list of suggested terms, you may browse the WPO using the WormBase Ontology Browser (WOBr). To use WOBr and view the ontology, click on "Browse the Phenotype Ontology" below either of the phenotype fields to be directed to the WormBase Ontology Browser page:


WormBase Ontology Browser.png


Click on the "+" symbol to the left of the root term "Variant" and subsequent terms to open up the Phenotype Ontology and begin browsing:


WPO in ontology browser.png


If you still cannot find an appropriate phenotype term, click on the check-box to the right of the text "Can't find your Phenotype?" to open up the "Suggest Phenotype" fields. Enter the name and definition of a suggested new phenotype term in the indicated fields:


Suggested phenotype.png


A WormBase curator will be notified and will confirm the new phenotype. Once a phenotype has been selected or suggested, enter any pertinent comments about the phenotype with respect to the allele entered above into the "Phenotype Remarks" field:


Phenotype remark.png


For WPO terms selected in the phenotype fields, a term information panel will appear in the upper right corner of the page displaying additional information about the phenotype selected as well as links to the WormBase phenotype page showing alleles known to exhibit this phenotype:


Phenotype term info.png

Optional Fields

Below the mandatory fields of the form are a series of fields for optional data, mostly pertaining to the nature of the allele with respect to the phenotype(s) indicated:


Optional section expanded.png


The first field is the "Inheritance Pattern" field, where users may use a drop down list to indicate whether the allele exhibits a recessive, dominant, or semi-dominant inheritance pattern:


Optional section-inheritance pattern dropdown.png


The next field is the "Mutation Effect" field, where users may use a drop down list to indicate the effect of the mutation on the phenotype, e.g. loss of function, gain of function, null, etc. :


Optional section-mutation effect dropdown.png


The last drop down list field in the Optional section is the "Penetrance" field, where users may indicate the degree of penetrance observed for the allele-phenotype pair indicated in the top section of the form:


Optional section-penetrance dropdown.png


Below the "Penetrance" field are two check boxes where users may indicate whether the allele is temperature sensitive (heat or cold sensitive) with respect to the phenotype. Lastly, there is a general comments field where submitters may indicate to WormBase curators any additional information important for the annotation:


Optional section filled out.png


Preview and Submission

Preview

Once all desired fields have been filled, click on the "Preview" button to see a preview of the data submission and check that the data was entered and recognized properly:


Preview summary table.png


Submission

When ready, click the "Submit" button and the data will be submitted to the Postgres database. The user will be directed to a submission confirmation page:


Submission confirmation.png


and will receive an e-mail summarizing the content of the submission:


Confirmation email.png


If the submission was unauthorized, recipients may click on the "Click here if you did not submit this data" to report the submission as unauthorized. Clicking on this link will direct to a confirmation page:


Unauthorized submission confirmation.png

Form population of Postgres and Phenotype OA

Dependency Notice: The Community Phenotype Form and the RNAi OA each have separate code to look up the most recent RNAi ID and generate new RNAi IDs based on that. If the code is changed for one, we should also check that the code is changed for the other.

Each allele-phenotype pair submitted via the Allele-Phenotype form will be submitted to the Phenotype OA and Postgres as a single entry with a unique Postgres ID (PGID). This means that multiple phenotypes (observed or not) submitted for a single allele via the form will be entered as separate PGIDs but all with the same shared fields, including community curator name and ID, allele, paper ID and all optional fields. The fields of the form correspond to the Phenotype OA fields in the following manner:


Allele-Phenotype Form Field --> Phenotype OA Field (Postgres table name)

Phenotype OA TAB 1

  • N/A --> Curator (app_curator) defaults to "Community Curator (WBPerson29819)" for every submission
  • Your Name --> Community Curator (app_communitycurator)
  • Your E-mail Address --> Community Curator Email (app_communitycuratoremail)
  • PubMed ID --> Pub (as WBPaper ID) (app_paper) OR Unregistered Paper (if unrecognized) (app_unregpaper)
  • Allele --> Variation (app_variation) OR Unregistered Variation (if unrecognized) (app_unregvariation)
  • Comment (Optional section) --> Object Remark (app_obj_remark) [not dumped]
  • "NO DUMP" (app_nodump) and "Needs Review" (app_needsreview) toggled ON by default for every submission

Phenotype OA TAB 2

  • Observed Phenotype --> Phenotype (app_term) (NOT toggled OFF) (app_not)
  • Phenotype Remark --> Phenotype Remark (app_phen_remark)

Phenotype OA TAB 3

  • Inheritance Pattern --> Allele Nature (app_nature)
  • Mutation Effect --> Functional Change (app_func)
  • Penetrance --> Penetrance (app_penetrance)
  • Heat Sensitive --> Heat Sensitive (app_heat_sens)
  • Cold Sensitive --> Cold Sensitive (app_cold_sens)

Phenotype OA TAB 4

  • Suggested Observed Phenotype --> Suggested (app_suggested) (NOT toggled OFF) (app_not)
  • Suggested Definition --> Suggested Definition (app_suggested_definition)


Currently (as of July 1, 2015), all submissions through the Allele-Phenotype form will send an e-mail to the submitter and to Chris Grove, and the "NO DUMP" and "Needs Review" toggles will be turned ON by default. Community curation submissions through this form can be queried by querying for the "Community Curator (WBPerson29819)" and those in need of review can be queried via the "Needs Review" toggle. A history of all submissions to the form can be viewed at:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/data/allele_phenotype_history.html

Code documentation

Files on Mangolassi/Tazendra required for the Allele-Phenotype form:

  • CGI script (/home/azurebrd/cgi-bin/forms/allele_phenotype.cgi)
  • Javascript (/home/azurebrd/public_html/javascript/allele_phenotype.js)
  • Images file (/home/azurebrd/public_html/images)
  • History file (/home/azurebrd/public_html/cgi-bin/data/allele_phenotype_history.html)