Contributing Phenotype Connections
The following documentation explains the use and backend for the Phenotype form found here:
- 1 User Guide
- 1.1 Finding the Phenotype form
- 1.2 Overview
- 1.3 Required information
- 1.4 Optional Fields
- 1.5 Preview and Submission
- 2 Form population of Postgres and OA
- 3 Code documentation
Finding the Phenotype form
There are two main ways to reach the Phenotype form from the WormBase homepage. First, and most directly, you can click on the "Phenotypes" 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 "Phenotype Data Submission":
The first part of the 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, a genetic perturbation (at least one of RNAi, allele or transgene), and a phenotype (observed or not observed):
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, RNAi clone, or transgene 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 are also fields for genetic background (genotype or strain) and 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.
The form minimally requires a submitter's name and e-mail address, a publication's PubMed ID, a genetic perturbation (allele, RNAi, or transgene), 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.
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:
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.
This form requires the entry of a PubMed ID (or D.O.I. if no PubMed ID exists) for the publication in which the 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:
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:
The publication summary page consists of two tables: the top table lists papers for which WormBase data-flagging pipelines have predicted the presence of phenotype data:
There are two distinct pipelines that WormBase uses to detect and curate phenotypes: one for alleles and transgenes and another for RNAi phenotypes. Therefore, there are two indicators as to the status of each paper with regards to phenotype curation. The top status indicator reports the status with regards to allele and transgene phenotype curation and may read "flag this for Allele-Transgene phenotype data", "Allele-Transgene Curation in progress", "Allele-Transgene WormBase curated", or "Allele-Transgene Needs curation". Similarly, the bottom status indicator reports the status of the paper with regards to RNAi phenotype curation and may read "flag this for RNAi phenotype data", "RNAi Curation in progress", "RNAi WormBase curated", or "RNAi Needs curation". The "flag this for ... phenotype data" status indicates that our pipelines have not predicted this paper to contain that type of phenotype data; clicking on the link will flag the paper for phenotype data so that a WormBase curator can add it to the list of papers to curate. The "... Curation in progress" indicates that one or more community curators have submitted phenotype data for this paper but that the curation has not yet been completed by a WormBase curator. The "... WormBase curated" indicates that the paper has been completely curated (or is currently being curated) by a WormBase curator. The "... Needs curation" indicates that the paper has been positively identified to be reporting phenotype data, but no curation has begun.
The bottom table lists papers that have not been flagged for phenotype data.
The top table lists the curation status of papers for which WormBase data-flagging pipelines have predicted the presence of phenotype data, indicating that the paper either "Needs curation" (i.e. the paper has been flagged for phenotype data that has not been annotated), 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 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 phenotype data" will notify a WormBase curator that this paper has phenotype data and should be added to the list of papers considered as having phenotype data. Once clicked, you will be directed to a flagging confirmation page:
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:
but please continue with your submission, and a WormBase curator will contact you if there are any questions.
Each submission of data via this phenotype form requires at least one genetic perturbation to be indicated as responsible for the phenotype (observed or not). There are three types of genetic perturbations that the form will accept: RNAi reagents, alleles, and transgenes.
RNAi clone(s) or sequence(s)
An RNAi clone ID or sequence is required for submission of RNAi-phenotype data. You may enter a library name and gene name (e.g. "Ahringer dpl-1 clone"), the commercial clone well location (e.g. "Source BioScience II-6H13") or the sequence of the RNAi clone (e.g. "ACGTATGCTAG...."). You may provide multiple entries separated by commas.
Because RNA interference experiments can now be carried out in several species, the form has a species selection to specify which species the RNAi experiment(s) was/were carried out in, with a default to Caenorhabditis elegans.
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:
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:
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:
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 may contact you to confirm the existence of this allele.
A transgene name is required for submission of transgene-phenotype data. You may enter a WormBase-recognized transgene name or the name of an transgene that WormBase has not yet cataloged. Start typing a transgene name and suggestions will appear below the field:
Once a transgene is selected from the drop down list of WormBase-recognized transgene, a term information box will appear in the upper right-hand corner of the screen with additional information about this transgene:
This term information box displays links to the WormBase transgene page (via the WBTransgene ID).
Once a transgene has been selected/typed, a "Gene Causing Phenotype" field will appear to enter the gene in the transgene that is most likely responsible for the phenotype observed (e.g. overexpressed gene):
A notice will appear to the right of the field to indicate if a transgene name that has been entered is not recognized by WormBase:
If you are entering a "new" transgene name, click anywhere outside the field to set the name, and continue with your submission. A curator will be notified and may contact you to confirm the existence of this transgene.
By default, phenotype fields are displayed in the form for both observed and NOT observed phenotypes:
The "Not Observed Phenotype" field is reserved for phenotypes that were assayed for but were not observed (were wild type) for the RNAi clone(s), allele(s), or transgene(s) 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:
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. Once a phenotype has been selected or suggested, enter any pertinent comments about the phenotype with respect to the RNAi clone(s), allele(s), and transgene(s) entered above into the "Phenotype Remarks" field:
Note the presence of a "Personal Communication" checkbox which, if checked, indicates to WormBase that this phenotype was observed independently of any publication and should be considered a personal communication from the submitter (i.e. the paper ID will be ignored for this phenotype).
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 RNAi clones, alleles, and transgenes known to exhibit this phenotype:
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:
Click on the "+" symbol to the left of the root term "Variant" and subsequent terms to open up the Phenotype Ontology and begin browsing:
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:
A WormBase curator will be notified and will confirm the new phenotype.
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:
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:
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. :
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 phenotype indicated in the top section of the form:
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. Submitters are encouraged to specify the genetic background of the experiment either by typing the genotype into the "Control Genotype" field or by entering the name of the strain background in the "Control Strain" field. Lastly, there is a general comments field where submitters may indicate to WormBase curators any additional information important for the annotation:
Preview and Submission
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:
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:
and will receive an e-mail summarizing the content of the submission:
If the submission was unauthorized or accidental, recipients may click on the "Click here if you did not submit this data or would like to retract this submission" to flag the submission for omission. Clicking on this link will direct to a confirmation page:
Form population of Postgres and OA
Each allele-phenotype pair and transgene-phenotype pair submitted via the 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 or transgene via the form will be entered as separate PGIDs but all with the same shared fields, including community curator name and ID, paper ID and all optional fields. The fields of the form correspond to the Phenotype OA fields in the following manner:
Phenotype Form Field --> Phenotype OA Field (Postgres table name)
Phenotype OA - ALL TABS
- Observed Phenotype --> Phenotype (app_term) (NOT toggled OFF) (app_not)
- Not Observed Phenotype --> Phenotype (app_term) (NOT toggled ON) (app_not)
- Phenotype Remark --> Phenotype Remark (app_phen_remark)
Phenotype OA TAB 1
- N/A --> Curator (app_curator) defaults to "Community Curator (WBPerson29819)" for every submission
- PubMed ID --> Pub (as WBPaper ID) (app_paper)
- Allele --> Variation (app_variation)
- Transgene --> Transgene (app_transgene)
- Control Strain --> Strain (app_strain)
- Comment (Optional section) --> Object Remark (app_obj_remark) [not dumped]
Phenotype OA TAB 2
- Suggested Observed Phenotype --> Suggested (app_suggested) (NOT toggled OFF) (app_not)
- Suggested Not Observed Phenotype --> Suggested (app_suggested) (NOT toggled ON) (app_not)
- Suggested Definition --> Suggested Definition (app_suggested_definition)
Phenotype OA TAB 4
- 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 5
- Control Genotype --> Genotype (app_genotype)
Phenotype OA TAB 6
- Your Name --> Community Curator (app_communitycurator)
- Your Name --> Person (app_person) for each personal communication
- Your E-mail Address --> Community Curator Email (app_communitycuratoremail)
- PubMed ID --> Unregistered Paper (if unrecognized) (app_unregpaper)
- Allene Name --> Unregistered Variation (if unrecognized) (app_unregvariation)
- Transgene --> Unregistered Transgene (if unrecognized) (app_unregtransgene)
- "NO DUMP" (app_nodump) and "Needs Review" (app_needsreview) toggled ON by default for every submission
For RNAi-phenotype pairs, data will be submitted to the RNAi OA as follows:
Phenotype Form Field --> RNAi OA Field (Postgres table name)
RNAi OA - ALL TABS
- Observed Phenotype --> Phenotype Observed (rna_phenotype) (NOT toggled OFF) (rna_phenotypenot)
- Not Observed Phenotype --> Phenotype Observed (rna_phenotype) (NOT toggled ON) (rna_phenotypenot)
- Phenotype Remark --> Phenotype Remark (rna_phenremark)
RNAi OA TAB 1
- N/A --> Curator (rna_curator) defaults to "Community Curator (WBPerson29819)" for every submission
- PubMed ID --> Paper (as WBPaper ID) (rna_paper)
- RNAi Clone(s) or Sequence(s) --> DNA text (rna_dnatext)
- Control Strain (Optional section) --> Strain (rna_strain)
- Control Genotype (Optional section) --> Genotype (rna_genotype)
- Comment (Optional section) --> Remark (rna_remark)
RNAi OA TAB 2
- Suggested Observed Phenotype --> Phenotype Suggestion (rna_suggested) (NOT toggled OFF) (rna_phenotypenot)
- Suggested Not Observed Phenotype --> Phenotype Suggestion (rna_suggested) (NOT toggled ON) (rna_phenotypenot)
- Suggested Definition --> Suggested Definition (rna_suggested_definition)
- Penetrance (Optional section) --> Penetrance (rna_penetrance)
RNAi OA TAB 4
- Your Name --> Community Curator (rna_communitycurator)
- Your Name --> Person Evidence (rna_person) for each personal communication
- Your E-mail Address --> Community Curator Email (rna_communitycuratoremail)
- PubMed ID --> Unregistered Paper (if unrecognized) (rna_unregpaper)
- "NO DUMP" (rna_nodump) and "Needs Review" (rna_needsreview) toggled ON by default for every submission
Currently (as of December 17, 2015), all submissions through the Phenotype form will send an e-mail to the submitter and to Chris Grove, Karen Yook, and Gary Schindelman and the "NO DUMP" and "Needs Review" toggles will be turned ON by default in the respective OA's. 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:
Files on Mangolassi/Tazendra required for the Phenotype form:
- CGI script (/home/azurebrd/cgi-bin/forms/phenotype.cgi)
- Images file (/home/azurebrd/public_html/images)
- History file (/home/azurebrd/public_html/cgi-bin/data/phenotype_history.html)