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.edumailto: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-specie...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.orghttps://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.htmlhttps://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@gatech.edumailto:rbates8@gatech.edu m: 770.713.8531

From: GloBI globi-bounces@lists.gbif.orgmailto:globi-bounces@lists.gbif.org on behalf of John Oswald j-oswald@tamu.edumailto:j-oswald@tamu.edu Date: Monday, November 19, 2018 at 9:18 PM To: "globi@lists.gbif.org"mailto:globi@lists.gbif.org globi@lists.gbif.orgmailto: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.edumailto: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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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.htmlhttps://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@tamu.edumailto: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.orgmailto:globi-bounces@lists.gbif.org On Behalf Of Jorrit Poelen Sent: Tuesday, November 20, 2018 8:59 PM To: globi@lists.gbif.orgmailto: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-specie...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.orghttps://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.htmlhttps://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@gatech.edumailto:rbates8@gatech.edu m: 770.713.8531

From: GloBI globi-bounces@lists.gbif.orgmailto:globi-bounces@lists.gbif.org on behalf of John Oswald j-oswald@tamu.edumailto:j-oswald@tamu.edu Date: Monday, November 19, 2018 at 9:18 PM To: "globi@lists.gbif.org"mailto:globi@lists.gbif.org globi@lists.gbif.orgmailto: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.edumailto: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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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:

https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test...

or

https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nome...

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,

-jorrit

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/interact... translates terms native the iNaturalist into RO . https://github.com/globalbioticinteractions/inaturalist/blob/master/interact... 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/int... . 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@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

*From:*GloBI <globi-bounces@lists.gbif.org>
<mailto:globi-bounces@lists.gbif.org>*On Behalf Of *Jorrit Poelen
*Sent:* Tuesday, November 20, 2018 8:59 PM
*To:* globi@lists.gbif.org <mailto: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
<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@gatech.edu <mailto:rbates8@gatech.edu>

    m: 770.713.8531

    *From: *GloBI <globi-bounces@lists.gbif.org>
    <mailto:globi-bounces@lists.gbif.org>on behalf of John Oswald
    <j-oswald@tamu.edu> <mailto:j-oswald@tamu.edu>
    *Date: *Monday, November 19, 2018 at 9:18 PM
    *To: *"globi@lists.gbif.org"
    <mailto:globi@lists.gbif.org><globi@lists.gbif.org>
    <mailto: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 <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




    _______________________________________________

    GloBI mailing list

    GloBI@lists.gbif.org  <mailto:GloBI@lists.gbif.org>

    https://lists.gbif.org/mailman/listinfo/globi  <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.gbif.org_mailman_listinfo_globi&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=RumeEb9OhO5-uPYMBvLVR_6mx3SCkPawDJ-uJYJWSC4&s=RymsxaAO66KIoZRhT4qKmGNaLZuQhGlJY83ri2bvwfQ&e=>

---

GloBI mailing list GloBI@lists.gbif.org https://lists.gbif.org/mailman/listinfo/globi

Hi John -

Just to clarify: the list I shared in tabular form is the most recent, and full, list of biotic interaction terms as captured by the Relation Ontology today.  Biotic interaction terms are those that are categorized as "biotically   interacts with" at http://purl.obolibrary.org/obo/RO_0002437 .

My previous comment ("I am sure the list is incomplete") was to merely invite submissions for new terms if needed.

-jorrit

On 12/18/18 5:56 PM, John Oswald wrote:

Hi Jorrit,

See below…

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 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_oborel_obo-2Drelations_issues_295&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dueHTDSXJypeq0FI5lQj-v8NXbzS4gf6JC039fe2nsw&e= .

---Thanks for forwarding the request.

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

https://github.com/globalbioticinteractions/nomer/blob/master/nomer/src/test... https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_nomer_blob_master_nomer_src_test_resources_org_globalbioticinteractions_nomer_match_ro.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=bLOnkmZ-Oq5JmC7nW_pIrM2xdeQGi8klGvn-2QGHVpI&e=

or

https://raw.githubusercontent.com/globalbioticinteractions/nomer/master/nome... https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_globalbioticinteractions_nomer_master_nomer_src_test_resources_org_globalbioticinteractions_nomer_match_ro.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=1iHGLvubXqi0EY1ZO8BnnOrL_5o_D--oPUoq5lCjvgg&e=

---Thanks for this. But, to a systematist with world interests, this is a bit like just having access to a list of the species from one country. In order to evaluate how I might incorporate text and identifiers from the RO into my data capture, management, and sharing activities, I need to see the whole list. With only a partial list I don’t know how complete or incomplete the term-set in the RO is, so can’t evaluate its potential utility as a starting point for efforts on my end.

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 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_oborel_obo-2Drelations-23requesting-2Dnew-2Drelations&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=ZHSYxVNjDBCwzzZDQGY_xeoPClMCs9V1r-wtXtfwHxc&e= . If that is doesn't work for you, please feel free to share a list here and we can probably figure something out.

---As implied above, until I can see the complete list of terms it is not really possible to begin to assess what additions it might be useful to make to the existing set of relations.

Cheers,

John

Hope this helps,

-jorrit

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
<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro.obo&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=UybvNHx81p3DwazHuzsD6wMSjnksyOfABjQORy-_URs&e=>
and http://purl.obolibrary.org/obo/ro.owl
<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro.owl&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=cyZaEdfpg8XRDTA_uT_M3JfJt9zDCJkuNSPHdJC0MI0&e=>
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>
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jhpoelen_eol-2Dglobi-2Ddata_issues_386&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=S-CisqDftExwEZ8v8OLNYG8I8y_tPb5_E569M4nxEHs&e=>).
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>
<https://urldefense.proofpoint.com/v2/url?u=https-3A__api.globalbioticinteractions.org_interactionTypes.csv-3Ftype-3Dcsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=WJRJNW0hGM_OJgBtvYFJn2LANpVTRuH4UGYiYwp9njg&e=>
. 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=vfFj0sH8Q1u7SHFS8fr_Ftlv2LVRY6SmVjDa1Jbrk6Q&e=>
:
https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types.csv
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist_blob_master_interaction-5Ftypes.csv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=eK2zxDUlkmks2vwdBAQhS9LnfOo9bSLzkb4ZhGJa-No&e=>
translates terms native the iNaturalist into RO .
https://github.com/globalbioticinteractions/inaturalist/blob/master/interaction_types_ignored.csv
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_inaturalist_blob_master_interaction-5Ftypes-5Fignored.csv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=dyHroS0Jg3VwKa2K2uvcKDjZgUIs8uOtl47tDSXLUH4&e=>
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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_template-2Ddataset&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=2RaJvXtmF7EAnNl8f0B3GrpGykRYsndcs6P6Fr3hhfQ&e=>
and, more specifically in
https://github.com/globalbioticinteractions/template-dataset/blob/master/interactions.tsv
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_globalbioticinteractions_template-2Ddataset_blob_master_interactions.tsv&d=DwMDaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=n0isp79O1WSTtoOYJGr1_rF-2PrQuw41UXGiGQ_Rpb8&m=qe_jiiQq2Of1OAuPqNYQ2uIX0GtADtE74rHucbwkhRo&s=Ryx7Z2SNz7Ar7p58vJU1A0qpkstpPLY0kpGzxLJytuo&e=>
. 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@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

        *From:*GloBI <globi-bounces@lists.gbif.org>
        <mailto:globi-bounces@lists.gbif.org>*On Behalf Of *Jorrit
        Poelen
        *Sent:* Tuesday, November 20, 2018 8:59 PM
        *To:* globi@lists.gbif.org <mailto: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
        <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@gatech.edu <mailto:rbates8@gatech.edu>

            m: 770.713.8531

            *From: *GloBI <globi-bounces@lists.gbif.org>
            <mailto:globi-bounces@lists.gbif.org>on behalf of John
            Oswald <j-oswald@tamu.edu> <mailto:j-oswald@tamu.edu>
            *Date: *Monday, November 19, 2018 at 9:18 PM
            *To: *"globi@lists.gbif.org"
            <mailto:globi@lists.gbif.org><globi@lists.gbif.org>
            <mailto: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 <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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