materialSample data management

[ricklevy21]

In addition to our herbarium and fungarium, we house a tissue biorepository as well as keep DNA samples. Nearly all of the samples are associated with a specimen that is managed within Symbiota. It would fantastic if there were some means to manage the sample data within the Symbiota portals. For example, an Associated Material Sample section within the Linked Resources tab. I believe this would be different from the Genetic Resources tool, which is for linking specimens to GenBank records. A way to upload this data in bulk alongside specimen metadata would be useful, as well as including a materialSample data extension file in the downloads option.

some field to consider

• https://dwc.tdwg.org/list/#dwc_materialSampleID
• https://terms.tdwg.org/wiki/ggbn:materialSampleType
• https://terms.tdwg.org/wiki/ggbn:preparationType
• https://dwc.tdwg.org/list/#dwc_catalogNumber (could there be a catalogNumber field specific to this use, so as to not commingle with specimen records)
• http://data.ggbn.org/schemas/ggbn/terms/preparedBy
• http://data.ggbn.org/schemas/ggbn/terms/preparationDate

Happy to discuss further or help any way I can

Rick

[themerekat]

Thanks for this input and for the links to helpful fields. It seems that, because these DNA samples are in fact Genetic Resources, this request would entail a revamp of the current Genetic Resources tool such that these additional fields could be added along with the GenBank URLs.

Have any ideas for grants that could help fund the development of this? Not sure what other institutions are working with DNA samples, but I know they are common.

For future reference, developing materialSample extension is here: https://tools.gbif.org/dwca-validator/extension.do?id=dwc:MaterialSample

[themerekat]

@ricklevy21 , @kyule reports that they use the Occurrence Associations box within the Linked Resources tab to manage material samples. They have a separate collection of DNA samples in their portal, and they link the specimens to those DNA samples. That could be a good way to manage your tissue samples as well.

[ricklevy21]

@themerekat oh wow, the Occurrence Associations box has way more to it than I realized. Thank you for this tip, I will look into this!

[ricklevy21]

@themerekat I see that a Material Sample tab has emerged, at least on SEINet. No function yet, but is this a development I should keep my eye on?

[egbot]

Yes, this has been in development for a while. I should be able to activate this within your collections within the very near future

[ricklevy21]

Thanks @egbot , you are a hero!

[carmirac]

A way to upload this data in bulk alongside specimen metadata would be useful, as well as including a materialSample data extension file in the downloads option.

Can anyone point me to instructions on the upload portion of the OPs question? I was hoping to be able to just append the data to my existing database and upload it all together.

[themerekat]

There current is no way to upload associated occurrences / material sample data. Stay tuned!
If you have an immediate need, we can facilitate this on the backend, so let us know.

[ricklevy21]

It would be very useful to have a way to identify records with/without material samples in the Collection Management>Edit Occurrence>Record Search Form. A "with material sample" check box, much like the "with images" check box is one idea.

[themerekat]

Thanks! Just opened an issue for this idea