Contributing Allele Phenotype Connections

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

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:

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":

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):

The second part of the form carries fields for optional data, pertaining to the nature of the allele with respect to the observed phenotypes indicated in the form:

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.

Minimum required information for data submission

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.

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

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.

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

Once a 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:

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:

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

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:

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:

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:

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:

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.