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Re: [GloBI] Ontology of Biotic Interactions?
by Bates, Robert P 20 Dec '18

20 Dec '18

Hi John, We’ve been working with subsets of the OBO Relation Ontology (which if I’m not mistaken is also what GloBI uses) to provide the concepts for interaction relationships in our VERA modeling system: http://www.obofoundry.org/ontology/ro.html -R Robert Bates Research Scientist Design & Intelligence Lab Georgia Institute of Technology Technology Square Research Building, 85 5th Street NW, Atlanta, GA 30308 e: rbates8(a)gatech.edu<mailto:rbates8@gatech.edu> m: 770.713.8531 From: GloBI <globi-bounces(a)lists.gbif.org> on behalf of John Oswald <j-oswald(a)tamu.edu> Date: Monday, November 19, 2018 at 9:18 PM To: "globi(a)lists.gbif.org" <globi(a)lists.gbif.org> Subject: [GloBI] Ontology of Biotic Interactions? I’m growing and extending interaction/association data in my research database on the species of the superorder Neuropterida (Insecta: orders Neuroptera, Megaloptera, and Raphidioptera) of the world. The data is primarily drawn from the published literature; some also from specimen labels. I’m interested in standardizing the terminology that I use to describe interactions and associations. I’m interested in taxon to taxon interactions (e.g., species X eats species Y; species X is phoretic on species Y), taxon to inanimate object interactions/associations (e.g., species X oviposits on substrate Y [say, rocks]), and taxon to concept associations (e.g., species X exhibits behavior Y). Can anyone recommend any good lists of standardized terms (with definitions) for this sort of thing? Are there any good, well developed, ontologies for general taxon-taxon and/or taxon-inanimate interactions? I have a list of 500+ “association kinds” (without well-standardized definitions) that I have scraped together over the years. I’d like to plug these into (or convert them into) something more standardized if something more standard exists. Thanks for any suggestions on where I might go next on this. ---oo0oo--- John D. Oswald Professor of Entomology Curator, Texas A&M University Insect Collection Department of Entomology Texas A&M University College Station, TX 77843-2475 E-mail: j-oswald(a)tamu.edu<mailto:j-oswald@tamu.edu> Phone: 1-979-862-3507 Lacewing Digital Library: http://lacewing.tamu.edu/ Bibliography of the Neuropterida: http://lacewing.tamu.edu/Biblio/Main Neuropterida Species of the World: http://lacewing.tamu.edu/SpeciesCatalog/Main

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Ontology of Biotic Interactions?
by John Oswald 20 Nov '18

20 Nov '18

I'm growing and extending interaction/association data in my research database on the species of the superorder Neuropterida (Insecta: orders Neuroptera, Megaloptera, and Raphidioptera) of the world. The data is primarily drawn from the published literature; some also from specimen labels. I'm interested in standardizing the terminology that I use to describe interactions and associations. I'm interested in taxon to taxon interactions (e.g., species X eats species Y; species X is phoretic on species Y), taxon to inanimate object interactions/associations (e.g., species X oviposits on substrate Y [say, rocks]), and taxon to concept associations (e.g., species X exhibits behavior Y). Can anyone recommend any good lists of standardized terms (with definitions) for this sort of thing? Are there any good, well developed, ontologies for general taxon-taxon and/or taxon-inanimate interactions? I have a list of 500+ "association kinds" (without well-standardized definitions) that I have scraped together over the years. I'd like to plug these into (or convert them into) something more standardized if something more standard exists. Thanks for any suggestions on where I might go next on this. ---oo0oo--- John D. Oswald Professor of Entomology Curator, Texas A&M University Insect Collection Department of Entomology Texas A&M University College Station, TX 77843-2475 E-mail: j-oswald(a)tamu.edu<mailto:j-oswald@tamu.edu> Phone: 1-979-862-3507 Lacewing Digital Library: http://lacewing.tamu.edu/ Bibliography of the Neuropterida: http://lacewing.tamu.edu/Biblio/Main Neuropterida Species of the World: http://lacewing.tamu.edu/SpeciesCatalog/Main

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blog post "Models in Fashion"
by Jorrit Poelen 17 Aug '18

17 Aug '18

Hey y'all - I just posted a first pass at a blog post that gives some examples of the many data formats used to capture species interactions. First two paragraphs from https://www.globalbioticinteractions.org/2018/08/16/models-in-fashion/ : "GloBI adapts to whatever contributors decided to express their digital data in and currently supports over 40+ flavors of species interaction data formats. This makes GloBI both fashionable and unfashionable – newer, hipper formats/models are supported as well as those that have been around for a while. Being fashionable has the advantage of appealing to the new hip kids in town. Supporting the older formats, however, might actually be crucial to preserve valuable datasets from previous generations. In this post, I’ll give some examples of formats currently used to share species interaction datasets. To help navigate through the various approaches, examplar datasets are described that fit into the following categories: single tabular text file, multi-tabular text files, json, rdf/owl/json-ld, and Darwin Core Archives. And, I’ll end with sharing some closing thoughts." Curious to hear your thoughts! thx, -jorrit

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Desert Island, Elton, Nomer and other updates
by Jorrit Poelen 12 Mar '18

12 Mar '18

Hey y'all - Just wrote a blog post on Desert Island, following a question I got at a workshop in Bari, Italy in Feb 2018 (some weeks ago). The blog post, https://www.globalbioticinteractions.org/2018/03/10/desert-island/ talks about the intent of GloBI. Also, it talks about two new tools: Elton and Nomer. Curious to hear your thoughts, -jorrit

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GloBI + spark + wikidata + taxon links
by Jorrit Poelen 05 Jan '18

05 Jan '18

Hey y'all - Just wanted to share some experiments I did using guoda / spark and wikidata: Today, after loading the wikidata archive into hdfs, I've extracted all taxon items (~2M) from wikidata and associated taxon ids (e.g., gbif, itis) in less than about 5 minutes. You should be able to reproduce this using https://jupyter.idigbio.org and my notes at https://github.c om/bio-guoda/guoda-datasets/tree/master/wikidata . Reason for my interest is to link GloBI into wikidata taxon items (e.g., https://www.wikidata.org/wiki/Q140), to retrieve associated data (e.g., images, common names) and to be able to share species interaction data with wikidata using their native ids (e.g., https://gi thub.com/jhpoelen/eol-globi-data/issues/209). I am sure other projects have similar needs. Needless to say, I would have been unable to do this data experiment without the guoda systems that are up and running. Curious to hear your thoughts and hope you find this inspiring, -jorrit > > > > > >

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