[GloBI] Ontology of Biotic Interactions?

Jorrit Poelen jhpoelen at xs4all.nl
Wed Dec 19 01:54:31 CET 2018

Hey John -

I've shared your desire to get a table of interactions terms of the 
Relations Ontology (RO) with Chris Mungall, the maintainer of RO (cc-ed) 
via https://github.com/oborel/obo-relations/issues/295 .

Meanwhile, I've created a minimal table of RO interaction terms for you 
to consider:




If you have suggestions on adding terms (I am sure the list is 
incomplete), please do share / document them via 
https://github.com/oborel/obo-relations#requesting-new-relations . If 
that is doesn't work for you, please feel free to share a list here and 
we can probably figure something out.

Hope this helps,


On 11/27/18 3:41 PM, Jorrit Poelen wrote:
> Hi John:
> Thanks for sharing the access database file. I was able to convert the 
> file to tsv files without too much trouble and had a look at the 
> examples you shared.
> I appreciate how you normalized the life stages and sex of the 
> interacting things. also, the reverse interactions and the pairs help 
> to more intuitively understand and parse the data.
> Re: associationTypes - When looking at the association kinds (from 
> tblAssocKinds), I realized that bodyPart (e.g., "leaf"), life stage 
> (e.g., "nymph") and physiological state (e.g., "dead") are mixed into 
> the interaction type (e.g., "feeding on"). I can see how this notation 
> can be handy for data entry or capture writing on labels, however, I 
> would have the tendency to map the interaction phrases to separate the 
> different kinds of things into separate columns, just like you did 
> with lifestage and sex.  That said, I'd always want to keep the 
> verbatim interaction phrase around to preserve the original language.
> Re: list of OBO relations terms - they are listed, but in specialized 
> formats (e.g., OBO, OWL) at http://purl.obolibrary.org/obo/ro.obo and 
> http://purl.obolibrary.org/obo/ro.owl respectively. I've opened an 
> issue to remind myself to make it easier to provide a list (see 
> <https://github.com/jhpoelen/eol-globi-data/issues/386>). For the time 
> being, you might be inspired by a subset of the supported interactions 
> types via 
> <https://api.globalbioticinteractions.org/interactionTypes.csv?type=csv> 
> . More on that later.
> Re: mapping interaction terms - I agree that automated mapping is 
> tricky business. What I had in mind is more of a static translation 
> table that is used to maintain how one systems interaction terms (like 
> yours) would translate into another naming scheme (like OBO Relations 
> Ontology). In our case, an automation would use the static translation 
> table to link the RO terms. So, no fancy methods here. An example of 
> such a translation table can be found at 
> https://github.com/globalbioticinteractions/inaturalist : 
> https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv 
> translates terms native the iNaturalist into RO . 
> https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types_ignored.csv 
> contains a list of terms that are explicitly ignored.
> Re: next steps - in my experience, highly normalized data structures 
> are important and useful when actively managing and curating data. 
> However, when exporting data to other systems, often a denormalized 
> format (aka "wide single table") really makes life a lot easier for 
> moving snapshots of the data around . . . as long as it's automated 
> and the identifiers are preserved. So, my suggested next step in our 
> integration would be to figure out how to create a method that 
> automatically generates a de-normalized table from your wealth of 
> association data in a similar form as outlined in 
> https://github.com/globalbioticinteractions/template-dataset and, more 
> specifically in 
> https://github.com/globalbioticinteractions/template-dataset/blob/master/interactions.tsv 
> . Once the de-normalization is complete, terms (like assocKinds, but 
> also lifestage, bodypart, physiological state) can be translated using 
> static translation tables (see above).
> In short - in my view, an integration would preserve the autonomy of 
> local data management, including terms, while automating a translation 
> into a de-normalized format friendly for integration. This allows to 
> updates to easily flow through the system without manual intervention 
> without effecting the existing data management platform. Most 
> importantly perhaps, the process contains sufficient information for 
> GloBI (or others) to link back into your database as well as the 
> original sources / specimen.
> I hope this helps and I'd be interested to help document this 
> integration between your Neuropterida database with GloBI as a use 
> case to share with our peers.
> Curious to hear your thoughts,
> -jorrit
> On 11/27/18 12:29 PM, John Oswald wrote:
>> Hi Jorrit,
>>      See below…
>> I think that sharing the Access database file would be a great start.
>> ---I have just shared a Dropbox folder with you that contains an 
>> Access database that contains the several tables that I am currently 
>> working with to try to formulate a strategy for capturing 
>> relationship data. I’m happy to receive any comments/suggestions for 
>> improvements. The three tables are briefly discussed below.
>> tblAssocKinds (association kinds) – Contains a list of 544 
>> “association kind” text strings. Many (ca. 200) of these originated 
>> with an initial 2010 dataset of associations that had been extracted 
>> from insect specimen labels by Norm Johnson of Ohio State University. 
>> I subsequently tried to standardize the phrasing of the original 
>> association strings, added additional strings, then tried to write 
>> “reverse association” strings so that there were pairs of phrases 
>> that could be used to state the relationship from the “opposite 
>> sides” of the association. The pairings are held in tblAssocPairs. 
>> Not all AssocKinds have reverse associations, so some are not 
>> currently included in a pair. The AssocKinds are mostly 
>> taxon-to-taxon or taxon-to-inanimate, but there are some outliers as 
>> I was experimenting with different kinds of associations. Is this 
>> kind of “reverse association” information useful in a broader context?
>> tblAssocPairs (association pairs) – Contains pairings of values from 
>> tblAssocKinds.
>> frmFlexAssocPairs – A simple query that contains AssocPairs as both 
>> AssocKind IDs and text strings (easier to read).
>> tblAssociations – My current working table for capturing association 
>> data from the literature. This table currently contains only ca. 150 
>> records of test data entered from the literature (I want to make sure 
>> that I get things set up optimally before extending the data capture 
>> effort). The table is general structured around a “left” associate 
>> and a “right” associate, “separated” by an AssocPair ID that links to 
>> tblAssocPairs. The table is currently structured for ease of data 
>> capture from the literature, and includes some other kinds of 
>> desirable data (e.g., sex, life stage, geography, literature source) 
>> that would be captured from the same literature sources. As I get 
>> into this though, it seems clear that many of those other data, which 
>> will not be available for all associations, should probably be 
>> removed to other relationally-linked tables in order to keep the data 
>> normalized. In the current structure the “left” associate is assumed 
>> to be an insect species of the superorder Neuropterida, which is 
>> specified by a “combination object” ID (field LeftNidaCombObjID). For 
>> data entry purposes this ID links to an episodically re-calculated 
>> lookup table of >20,000 genus-group/species-group scientific name 
>> combinations (essentially a master lookup table of almost every 
>> Neuropterida combination that has ever been used in the literature). 
>> This “combination” ID can be used to link into most of the related 
>> taxonomic and nomenclatural data in my database. The link to the 
>> literature source is specified in field BibObjPageCiteID 
>> (Bibliographic Object Page Citation ID), which is an identifier that 
>> specifies a particular page/plate in the neuropterid literature (from 
>> which can be looked up all of the typical bibliographic information 
>> about the literature source, plus other data linked to individual 
>> literature pages, e.g., figures, chresonyms, and other annotations). 
>> This links to my bibliographic dataset of 17,000+ published works 
>> that contain information on the Neuropterida.
>> 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).
>> ---To the extent possible I would prefer to not have to rely on 
>> automated translations, which are prone to interpretation errors (or 
>> maybe I’m misunderstanding what is automated here…). I would prefer 
>> to “oversplit” the associations that I use in my database, then 
>> re-group those associations into aggregate sets that correspond to 
>> other set(s) of association types used by other projects. This would 
>> give me more flexibility for defining associations that are useful 
>> for my purposes, and more control over how those associations are 
>> mapped when used in (potentially multiple) other contexts. We’re 
>> probably saying basically the same thing here, but I would like to 
>> retain the ability to control/influence the basic mapping of 
>> associations through relationships defined in my database.
>> 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 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__obofoundry.org_ontology_ro.html&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=SYaRVnY0jiGjyYGGuj4Lx0dPncmBZFAatHgtwJ-h4Uk&s=so-xkW80dqsEkKPNLOdRhe1JCD0nC8HQgpn-zKjmaDE&e=>): 
>> the closer the terms are in meaning, the easier the mapping is.
>> ---Right, see above. How can I get a complete listing of the relation 
>> strings used in the Relation Ontology, their definitions (meanings), 
>> and their hierarchical organization? I don’t know how to do that. Is 
>> that something you can conveniently download, put into a table-based 
>> format, then send to me so that I can incorporate it into my database 
>> to experiment with?
>> ---I expect that the relations in the Relation Ontology are fairly 
>> general. Is there another ontology (or some other source of relation 
>> terms) that deals more specifically (or at least includes) more 
>> specific relations that would pertain between insect taxa and either 
>> insect or non-insect taxa, and/or insect taxa and inanimate objects? 
>> That is something that I would find useful. Does something like that 
>> exist? Outside of the Relation Ontology, where do you source other 
>> kinds of relations? Or, how does one go about contributing to the 
>> development of a more specific ontology of relations that pertain to 
>> insects? Would that be a useful thing?
>> 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.
>> ---I’m interested to know if others have already developed 
>> well-defined sets of terms/phrases that describe 
>> relations/associations among insects and other organisms and 
>> inanimate objects. Can you make any recommendations for where I might 
>> look to find to find such sets of terms/phrases? Do any of the other 
>> projects involved in GloBI have such term/phrase sets that are 
>> available for examination?
>> 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 like.
>> ---You should have received an e-mail from Dropbox on this today, or 
>> will soon.
>> Cheers,
>> John
>> Curious to hear your thoughts,
>> -jorrit
>> 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>
>>     <mailto: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 <mailto: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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