Hi Jorrit,
Thanks for responding. Deborah Paul mentioned to me at the recent ESA meeting in Vancouver, BC, that GloBI would be one place that I should look, so I hoped to make contact with you by posting to the GloBI
listserver. See more interleaved below…
---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@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
From: GloBI <globi-bounces@lists.gbif.org>
On Behalf Of Jorrit Poelen
Sent: Tuesday, November 20, 2018 8:59 PM
To: globi@lists.gbif.org
Subject: Re: [GloBI] Ontology of Biotic Interactions?
Hey John -
Like Robert (hi Robert!) mentioned, GloBI is also using the OBO Relations Ontology for defining biotic and abiotic interaction types, just like many other projects.
---As a newbie to ontologies (and an entomologist, not a computer scientist) I’m still trying to wrap my head around ontologies. In a nutshell, so far as I can determine, an ontology is at heart an extended web of controlled vocabulary
terms with relationships defined between terms at different web nodes (terms), together with facilities to link to other ontologies. Is that about right?
I've been attempting to collect my thoughts on data format and models at
https://github.com/jhpoelen/globis-b-interactions/blob/master/text/on-species-interaction-data-models-and-formats.md .
---Thanks for the link. I have briefly looked this over just now, but will go back for a detailed read later. There appears much there that would be good for me to consider as I continue development on my end.
In my experience, an effective way to figure out how to capture/share your data is to use what you have today (as is!) and try to integrate a subset of it with other projects (like GloBI, GBIF).
---For the present, as briefly explained in my initial e-mail, I’m mostly trying to set up an efficient way to capture data on interactions/associations of neuropterid species with other taxa, inanimate objects, and concepts in
my personal Neuropterida research database on the three insect orders Neuroptera, Megaloptera, and Raphidioptera. The Neuropterida database (currently built in Access) is highly parsed (ca. 350 relationally linked tables, including ca. 150 standardized ‘lookup’
tables covering various subjects), and significantly normalized (ca. 300 tables normalized to 3NF or better). The core data are bibliographic, nomenclatural, taxonomic, and ‘agent based’, but there are extensions going off in many other directions. I currently
share parts of these data via episodic downloads to support a variety of projects – particularly the Neuropterida domain of the Catalogue of Life (used by GBIF and many other projects globally), and the various modules of the Lacewing Digital Library project
(lacewing.tamu.edu). I am an insect systematist/taxonomist by training, but I got into databasing in the early 1990’s and have been capturing data on the Neuropterida ever since. I am currently involved in a project whose primary product will be a new module
in the Lacewing Digital Library that is devoted to interactions/associations (mostly predator/prey) of neuropterid insects and hemipterous insects. Thus, my primary motivation at the current time is to develop an effective and efficient database subschema
for capturing these kinds of data, and to relationally link that subschema into my existing overall database schema. I would like to do this in a fairly general way so that I can (1) capture a wide variety of different kinds of interaction/association data
into the same subschema of my database, (2) standardize the terminology/phrasing that I use so that terms/phrases are based on explicit definitions and are consistent with other similar controlled vocabularies for similar projects (to the extent that this
may be possible; thus my foray here into ontologies…), and (3) be reasonably sure that there is fairly straightforward pathway through which whatever interaction/association subschema I develop within my database that it can be linked out to other projects
that I might get involved with in the future.
Your projects sounds very similar to other projects that have already been integrated into GloBI - a mix of specimen and literature data with their own way of describing interaction terms.
---Yes, I am sure that there are lots of other projects that are capturing similar data. I’d like to learn from those projects so that I can avoid any common pitfalls and ‘start off on the right foot’ as I get into this. To the
extent possible, as I get started, I’d like to tap into any well-defined sets of interaction terms that may already exist. My initial though has been to build out this subschema in my database starting from my current table of ‘association kinds’. But I’m
open to new ideas, and looking for someone who might be interested to discuss such issues.
Do you have some samples that you can share so that I can get a sense of what you currently have?
---Sure. I can export a few tables to a simple Access database and send that to you. Can you work with that? Please confirm. If so, I can e-mail it to you or post it to you via Dropbox (depending on size).
---One of the difficulties that I am currently having is how one might extract the “data items” (to me this would be the set of controlled terms/phrases and their linking interaction/association terms) from one or more ontologies
so that those data can be placed into and manipulated within a relational database structure. Is there an easy way to do that?
Cheers,
John
thx,
-jorrit
https://globalbioticinteractions.org
On 11/19/18 6:21 PM, Bates, Robert P wrote:
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
m: 770.713.8531
From: GloBI <globi-bounces@lists.gbif.org> on behalf of John Oswald <j-oswald@tamu.edu>
Date: Monday, November 19, 2018 at 9:18 PM
To: "globi@lists.gbif.org" <globi@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@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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