Submit Phenotype Data
PharmGKB accepts submissions of phenotype data - which include data regarding clinical outcomes, pharmacodynamics and drug responses, pharmacokinetics, and molecular and cellular functional assays - in Microsoft Excel workbook form. All phenotype data submissions must comply with the PharmGKB phenotype templates. There are 4 distinct templates for different data types:
- Subject or sample based data- where the phenotypes relate to an individual or cell line with a PharmGKB Accession ID. Each row in this file corresponds to a Subject or Sample. For an example file see Hot flashes in tamoxifen patients.
- Artificial Constructs- where the phenotypes relate to the activity of a promoter reporter construct containing a gene promoter sequence, or an expression construct containing a gene or part of a gene expressed in a cell system. For an example file see ABCB1 Functional Protein Variants.
- Named Alleles- where the phenotypes relate to constructs that express variants with well described star allele nomenclature. For an example file see CYP2C9 Variants and Naproxen Metabolism.
- Proteins - where the phenotypes relate to purchased recombinant proteins. For an example file see Meperidine N-demethylation by human CYP450 isoforms.
If your data does not conform to these templates, please contact us. It may be possible to submit the data as an attachment file. High impact files will be curated and integrated into the PharmGKB database. If the file cannot be readily integrated, it will be posted as a full-text indexed attachment.
Submitting phenotype data to the PharmGKB can be broken down into five steps:
- Send email to submission@pharmgkb.org and attach a completed Excel template.
- PharmGKB curators will assist you with standardizing the format and terminology of the phenotype file so that it is consistent with other data in PharmGKB.
- The revised file will be posted on the PharmGKB Preview website, where you can verify your data.
- If you are satisfied, the PI of the project must go to the PharmGKB Preview website and click the "Approve Submission" button on the submission page containing the data.
- The approved file will be posted on the PharmGKB public website.
Phenotype Submission Template
PharmGKB accepts phenotype data in Microsoft Excel workbook form. All phenotype templates contain two pages.
First Page
This page is the "legend" sheet and is basically the same for all four phenotype templates. It contains meta-data about the submitted data, including the submitting group, references, and a brief description of the goal of the study and the data being reported. The data description can also be the abstract from the reference paper. On this page, the genes, drugs and diseases associated with the study are also listed.
At the bottom of the page, you will find the legend for the columns of data found on page two of the workbook. The column abbreviations should be entered exactly as they appear on page two. All abbreviations should then be defined on the first page in the legend. Any additional information about how the data values were calculated, how the values are reported (including units of measurement), how to interpret missing data values, etc., should be defined on this page as well. Definitions of the columns and data are necessary for others who are not extremely familiar with the subject matter to understand and make use of the data.
The "Categories of Pharmacogenetic Knowledge" that best represents the data should be entered on this page. More than one category can be selected if appropriate.
Phenotype data is further annotated with one or more "Phenotype Classification" labels. These labels are found in the "Pharmacogenetics Ontology" on the PharmGKB website. The phenotype ontology lists types of phenotype data that investigators are known to be collecting. This ontology may be expanded to accommodate new types of phenotype data. If you are conducting research in an area that you feel is not represented by this ontology, please send email to our curators.
Second Page
This page of the workbook contains the data itself. Subjects/artificial constructs/named alleles/proteins are represented by rows and phenotype data are represented by columns.
Columns can be labeled with abbreviations, which should be defined on the "legends" page (first page) of the workbook.
For subject data only:
PharmGKB Accession IDs can be obtained by emailing PharmGKB with the number of IDs needed. Please inform us if you are using samples from Coriell or another repository, as PharmGKB does not want to assign subjects multiple ID numbers.
Any data considered sensitive or that could compromise the subjects' identities will be re-formatted, with the help of the submitter, before posting on the website. For example, if age information is included, it should be submitted as an age range rather than as an exact number. Please select from the following ranges: 0-9, 10-19, 20-29, 30-39, 40-49, 50-59, 60-69, 70-79, 80-89, 90+.
Reviewing and Approving Submitted Data
Only project PIs and other pre-approved registered users are able to approve submissions. The user with approval permissions must login to the PharmGKB Preview website.
Then:
Click on the "Search" tab at the top of the page. Click on the "Submissions by project" link. Find your project and click on the number in the "Pending" column. Click on the submission ID (PS number) that you would like to approve.
OR
If you know the submission ID of the submission you want to approve, type it into the search box at the top right corner of the page. A search page should come up listing that submission. Click that link to continue.
Once on the submission page, click the "Approve Submission" button on the page. If there is a problem with the submission, you can reject the submission by clicking on the "Reject Submission" button instead.
Note that only project PIs and other pre-approved registered users are able to view the Approve and Reject buttons, because they are the only users allowed to approve or reject submissions.