Have you come across an error when you’re glancing through the study pages of OSDR? Maybe you see a typo. Maybe there’s more. Let’s give you a public place to report any errors that you catch.
Here’s a link to a spreadsheet. Anyone should be able to edit this.
We do not presently have the humanpower to tackle these reports. But maybe we will be allotted more time to do this if we have a running list.
We DO make changes to pages when:
The original submitter or an author that they list makes a new version themselves and asks us to review it - if you do not have access to a page that you’re an author on, let us know and we can guide you through the process of being added!
We are given data for a related study and that submitter indicates that they want specific older studies to be readily comparable.
Probably other reasons I can’t even imagine.
And… if someone happens to be making edits to those pages for other reasons, it would be nice to have a list for us to look at and see if we can make those suggested changes as well!
Hi @botanynerd i found this variation in how VEGGIE hardware name is recorded, 14 studies, 6 very similar ways of writing the name of the hardware. * OSD-177
There are a lot of ways to write BRIC / petri dish fixation unit (PDFU), the BRIC-LED is also a distinct variant… OSD-17, OSD-37, OSD-38, OSD-44, OSD-121, OSD-138, OSD-145, OSD-147, OSD-185, OSD-205, OSD-321, OSD-500 and OSD-522.
There seems to be some issues with the GeneLab DOI in the BibTex and RIS files automatically generated by GeneLab for the projects, replicated in MyBib, Hayagriva, and Zotero:
There seems to be a specific “Database name” parameter in the bibtex and ris files that is separate to the publisher parameter. I assume these citation files should read “NASA OSDR, version x” for this parameter, which is just blank at the moment.
Author names in the generated bibtex and ris files default to the company/organization name format, at least in MyBib (screenshot w/example below). I’m not sure if there’s something in the format that specifies if it’s an author or an organization, or if this is an issue with MyBib handling these files. Hayagriva and Zotero seem to generate the correct citations, but they don’t allow me to check author/organization in the citation manager like MyBib.
The “url” (BibTex) and “UR” (RIS) parameters default to the actual OSDR website url (NASA OSDR: Open Science for Life in Space) instead of the DOI url (http://doi.org/10.12345/abcd-wxyz). This results in final citations with the OSDR website url instead of the DOI url, contrary to the example on the OSDR pages.
This is all very helpful. We know that there is a need to update a lot of metadata from older studies, and the ontologies especially need a lot of updates. Some of it is due to changes in ontology links over time due to “dead” links, but a lot of it is also because metadata was not kept as consistent across repo until we started having the tools and sufficient personnel to make significant efforts to standardize.
That being said, please keep tracking them in the sheet above. We will try our best to get to the updates as soon as possible. We have an internal glossary of ontology terms that we are using to make sure that we use the same tissue/species/etc ontologies across studies (which should fix the capitalization inconsistencies). Please track them in the spreadsheet so we know which ones need addressing!
I have also made several scripts to gather metadata for the various OSDR pages (studies, experiments, hardware, payloads, and missions). I can’t share the scripts here since they utilize the non-public API, but I can share the csv files if they help with error catching efforts.
Hi Rachel.
For OSDR 218, ~18 of the samples “Ground control” and the rest are “Ground Control”; the original typo came from the GEO import and the first half of the samples have correct capital letter use. Should be a easy fix that will greatly improve the multistudy viz.
Yep, it’s on my list of studies to update! Some of the older studies are taking a while to update since we have a lot of ISA framework-related revisions to do at the same time as metadata updates.
Hello again, i think the data pulled in from the ISA framework isn’t catching the full depth of the genomic and genetic varieties used in an experimental accession. Below is a screenshot showing the current GL-multi-study viz tool, hopefully, you see it can’t currently build a statistical model that captures both the ecotypes genomic feature and individual mutations collectively. In this example, we can see that the PhyD mutant has its ecotypic background incorporated (gold star), but the other mutants such as sku5, elp2-5, met1-7 don’t… Other than pulling the data down and working in one’s own dev environment i can’t think of an easy fix?
Should be a easy fix that will greatly improve the multistudy viz.
