Field Museum and iNaturalist Extending Specimen through DwC Resource Relationships

To extend ongoing conversations about extending specimen, I just shared a blog post on how the Field Museum and iNaturalist are extending their specimen / occurrences to capture species interaction data using a readily available DwC extension - the resource relationships.

Curious to hear your thoughts and comments.

How are you sharing your interaction data today?

Field Museum and iNaturalist Adopt Darwin Core Resource Relationship Standard to Share Species Interaction Records

The Field Museum and iNaturalist capture detailed records on how species interact. They both showed their capacity to innovate by using the recently improved Darwin Core Resource Relationship extensions to publish their interaction records. By using this standards based approach, they facilitate access to the valueable biodiversity knowledge they keep, and provide examples for others to follow. More …

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@jhpoelen thanks for this.

Some comments on A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/fmnh:

  • As a consumer of a bot created file I would like to be pointed to an issue tracker to provide this kind of feedback, at the top of the report.
  • In Methods I would like an ETA or size estimate of the resources I will be downloading or creating when I do elton based command. Maybe this is a feature request for elton (progress bars)?
  • In Methods I need to know if the method calls are idempotent, I ran the 4th first then realized I needed the data.

Several other things came up, apologies if I’m missing something obvious-

  • Sharing via resource relationships is noted in your article, yet I didn’t find reference to this format in the review, I found it a little difficult to figure out how these were related.
  • Is there an example of interactions.tsv in a DwCA archive?
  • Is there an example of interactions.tsv in a resource relationship format (i.e. referencing DwC fields in that extension)?
  • Is there a version of resource relationships that could be produced? Am I mistaken that we could use a resource relationship extension in asserting these data?

Finally, tacking this on, does anyone use resource relationships to make statements that are in the format?

subject_id predicate_id object label

For example I have UUIDs for a specimen (source), a PURL for a relationship, but only a taxon name (label for a concept) as the object (target). Example files would be wonderful.

Thanks again!

@matt We have this dataset on wildlife interactions (wildlife attacking domestic animals)

@vechocho thanks for pointing out your example of usage of the Resource Relationship extension to document wildlife interactions [1].

I was able to create a index configuration for this data via the RSS feed published by Ministerio del Ambiente, Agua y Transición Ecológica de Ecuador - MAATE .

Using this index configuration and an automated review workflow powered by GitHub Actions, the following review report was generated -

review-maate-2023-11-21.pdf (367.2 KB)

From which I learned that bears (Tremarctos ornatus) do like to eat their cows (Bos taurus), just like their competing apex predator Homo sapiens.

I’ve attached table 6. , figure 4.


You might notice interaction records exist in three other MAATE datasets [2,3,4]. These include road kills and plant associates, among others. For those, associatedTaxa fields are used.

References

[1] Registros de conflicto humano-fauna en Ecuador desde el año 2009 al
2022 - Version 1.2 http://patrimonio.ambiente.gob.ec/iptmae/archive.do?r=humano-fauna

[2] Caracterización de la Biodiversidad Microbiológica y de Invertebrados
de la Reserva Marina “El Pelado” a escala Taxonómica, Metabolómica
y Meta genómica para su uso en salud humana y animal - Version 1.6
http://patrimonio.ambiente.gob.ec/iptmae/archive.do?r=inmase_ce

[3] Colección de Plantas Vasculares del Herbario UTCEC - Version
2.0 http://patrimonio.ambiente.gob.ec/iptmae/archive.do?r=utcec-vasculares

[4] Colección de Vertebrados Estación Científica Charles Darwin - Ver-
sion 1.4 http://patrimonio.ambiente.gob.ec/iptmae/archive.do?r=vccdrs

Thanks for sharing that @vechocho, a nice straightforward example.

Thanks @jhpoelen for the analysis, we are using the Resource Relationship extension as we think let us give more information about the interactions.

Using the associatedTaxa field sometimes don’t let us explain what the relation is between two taxas.

This month we are going to have two more dataset using the extension, one on parasites on fauna (using a mammal as a bait) and other for bats and a virus presence.

@matt feel free to use the data for analysis and as you want for testing the model.

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@matt Thanks for taking the time to share your comments / observations re: GloBI data review of the interaction data shared by the Field Museum via their IPT.

Just wanted to let you know I saw your post, and that I am mulling over your comments and questions.

Thanks for being patient,
-jorrit

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Please let me know if these address your concerns.

@matt, I’ve attempted to address more of your notes / questions below. Curious to hear your thoughts.

Thanks again for your comments/ notes/ questions.

-jorrit