[GloBI] Ontology of Biotic Interactions?

Jorrit Poelen jhpoelen at xs4all.nl
Tue Nov 27 00:12:08 CET 2018

Hi John -

Thanks for sharing your detailed comments and providing background on 
your highly granular database.

I think that sharing the Access database file would be a great start. I 
imagine that a first GloBI integration (or any other integration) would 
preserve the existing system and implement an automated translation or 
mapping procedures (e.g., scripts). One of such procedures would include 
a mapping from your internal association types into another naming 
scheme such as OBO Relation Onology 
(http://obofoundry.org/ontology/ro.html): the closer the terms are in 
meaning, the easier the mapping is. With such a translation / mapping 
method in place, others can more easily find your data and you can more 
easily find similar projects. Then, hopefully, over time, we'll learn 
from each other in discussion forums, professional meetings or workshops 
and make it easier to share and capture these complex datasets. Perhaps 
we'll even settle on some best practices!

So, yes, please send a (complete/partial) copy of your native database 
files or raw datasets, so I can get a sense of what your datasets looks 

Curious to hear your thoughts,


On 11/21/18 11:32 AM, John Oswald wrote:
> 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 at tamu.edu <mailto:j-oswald at 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 at lists.gbif.org> *On Behalf Of *Jorrit Poelen
> *Sent:* Tuesday, November 20, 2018 8:59 PM
> *To:* globi at 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 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jhpoelen_globis-2Db-2Dinteractions_blob_master_text_on-2Dspecies-2Dinteraction-2Ddata-2Dmodels-2Dand-2Dformats.md&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=5rsVFs3GJwqHVhJgL9CJ3zhrFjEJuilAn7bu9SAW91c&e=> 
> .
> ---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 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__globalbioticinteractions.org&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=I3T9B7MwP8QsKCbpPfmjxbX37fWerqfnZPmO9RYlbCM&e=> 
> 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
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ontology_ro.html&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=kzb8EYNLqZjOBHOdXtKcwh141kUweLk_nINGFtUMVDc&e=>
>     -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 at gatech.edu <mailto:rbates8 at gatech.edu>
>     m: 770.713.8531
>     *From: *GloBI <globi-bounces at lists.gbif.org>
>     <mailto:globi-bounces at lists.gbif.org>on behalf of John Oswald
>     <j-oswald at tamu.edu> <mailto:j-oswald at tamu.edu>
>     *Date: *Monday, November 19, 2018 at 9:18 PM
>     *To: *"globi at lists.gbif.org"
>     <mailto:globi at lists.gbif.org><globi at lists.gbif.org>
>     <mailto:globi at 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 at tamu.edu <mailto:j-oswald at 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
>     _______________________________________________
>     GloBI mailing list
>     GloBI at lists.gbif.org  <mailto:GloBI at lists.gbif.org>
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