We find the orthology downloads very useful and were wondering where we could find documentation on the full parameters used with each tool to generate it? We would like to perform the same analysis and add other organisms (such as chicken).
Thanks -
Joshua
Hi Joshua,
The orthology data we use is derived from “DIOPT”, which stands for DRSC Integrative Ortholog Prediction Tool. Their website can be found here:
The DRSC is an organization founded by Norbert Perrimon, who is also the lead PI for FlyBase, one of the MODs of the Alliance. The documentation page on the DRSC website has a link to their most recent papers and a description of their methods:
For the Alliance website, we use a subset of the DRSC DIOPT data – so you’ll find small discrepancies between our data and the “original” DRSC DIOPT data. This is mainly due to our source data for the Alliance originating via the Quest for Orthologs initiative (https://questfororthologs.org/) which produces a different subset of starting data which are then processed by the various algorithms.
If you have any questions after looking over the DIOPT website, please let us know. You can also reach out to Dr. Claire Yanhui Hu (3rd person on this page: People | DRSC/TRiP Functional Genomics Resources & DRSC-BTRR). She’s responsible for managing the DRSC DIOPT website and all the associated source data.
From Claire Hu:
The original prediction files for ortholog calls were obtained from QFO benchmark site (Ortholog Benchmarking Webservice ) and chick is included. Need to let the user know that only 78 species are covered by reference proteome at this point (Reference proteomes < EMBL-EBI).
Claire
I’m glad to hear that you find the orthology downloads useful! To find documentation on the full parameters used with each tool to generate the orthology data and perform similar analysis, you would typically need to refer to the documentation and resources provided by the specific orthology database or tool you are using. Here are some general steps you can take to find the documentation:
Identify the Orthology Database or Tool: Determine which orthology database or tool you are using to access the orthology data. There are various databases and tools available, such as OrthoDB, EggNOG, Ensembl, OrthoMCL, etc. Each database/tool may have its own set of parameters and methods for orthology analysis.
Visit the Official Website: Go to the official website of the orthology database or tool. They often provide detailed documentation, tutorials, and user guides that explain the parameters, data formats, and usage of their tools.
Explore the Documentation Section: Look for a dedicated “Documentation” or “Help” section on the website. In this section, you should find information about the parameters used for orthology analysis and how to perform various types of queries or downloads.
Search for Tutorials or Examples: Some databases/tools offer tutorials or example analyses that showcase how to use their tools and interpret the results. These tutorials can be valuable resources for understanding the parameters and analysis workflows.
Contact Support or Community Forums: If you have specific questions or need further assistance, don’t hesitate to reach out to the support team of the orthology database/tool. They can provide expert guidance and help you with any issues you encounter.
Check for Academic Publications: In some cases, the developers of orthology databases/tools publish scientific papers or articles that describe the methods and algorithms used. These publications can provide in-depth insights into the tool’s parameters and analysis procedures.
Regarding adding other organisms, such as chicken, to the analysis, you would need to check if the orthology database/tool supports the inclusion of custom or additional species. Some databases/tools may have predefined sets of organisms, while others might allow you to upload or include your own data.
Remember that the specific steps and details may vary depending on the orthology database/tool you are using. By following the above steps, you should be able to access the necessary documentation and perform the desired analysis with additional organisms successfully.