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<p>Hi John - <br>
</p>
<p>Thanks for sharing your detailed comments and providing
background on your highly granular database.<br>
</p>
<p>I think that sharing the Access database file would be a great
start. I imagine that a first GloBI integration (or any other
integration) would preserve the existing system and implement an
automated translation or mapping procedures (e.g., scripts). One
of such procedures would include a mapping from your internal
association types into another naming scheme such as OBO Relation
Onology (<a class="moz-txt-link-freetext" href="http://obofoundry.org/ontology/ro.html">http://obofoundry.org/ontology/ro.html</a>): the closer the
terms are in meaning, the easier the mapping is. With such a
translation / mapping method in place, others can more easily find
your data and you can more easily find similar projects. Then,
hopefully, over time, we'll learn from each other in discussion
forums, professional meetings or workshops and make it easier to
share and capture these complex datasets. Perhaps we'll even
settle on some best practices!<br>
</p>
<p>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. <br>
</p>
<p>Curious to hear your thoughts,</p>
<p>-jorrit<br>
</p>
<div class="moz-cite-prefix">On 11/21/18 11:32 AM, John Oswald
wrote:<br>
</div>
<blockquote type="cite"
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<p class="MsoNormal"><span style="color:#1F497D">Hi Jorrit,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 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…<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">---oo0oo---<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">John D.
Oswald<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Professor of
Entomology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Curator,
Texas A&M University Insect Collection<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Department of
Entomology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Texas A&M
University<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">College
Station, TX 77843-2475<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">E-mail: </span><a
href="mailto:j-oswald@tamu.edu" moz-do-not-send="true"><span
style="color:blue">j-oswald@tamu.edu</span></a><span
style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Phone:
1-979-862-3507<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Lacewing
Digital Library: </span>
<a href="http://lacewing.tamu.edu/" moz-do-not-send="true"><span
style="color:blue">http://lacewing.tamu.edu/</span></a><span
style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Bibliography
of the Neuropterida:
</span><a href="http://lacewing.tamu.edu/Biblio/Main"
moz-do-not-send="true"><span style="color:blue">http://lacewing.tamu.edu/Biblio/Main</span></a><span
style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Neuropterida
Species of the World:
</span><a
href="http://lacewing.tamu.edu/SpeciesCatalog/Main"
moz-do-not-send="true"><span style="color:blue">http://lacewing.tamu.edu/SpeciesCatalog/Main</span></a><span
style="color:#1F497D"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="color:windowtext">From:</span></b><span
style="color:windowtext"> GloBI
<a class="moz-txt-link-rfc2396E" href="mailto:globi-bounces@lists.gbif.org"><globi-bounces@lists.gbif.org></a>
<b>On Behalf Of </b>Jorrit Poelen<br>
<b>Sent:</b> Tuesday, November 20, 2018 8:59 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:globi@lists.gbif.org">globi@lists.gbif.org</a><br>
<b>Subject:</b> Re: [GloBI] Ontology of Biotic
Interactions?<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Hey John - <span style="font-size:12.0pt"><o:p></o:p></span></p>
<p>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.
<o:p></o:p></p>
<p><span style="color:#1F497D">---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?<o:p></o:p></span></p>
<p>I've been attempting to collect my thoughts on data format
and models at <a
href="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="
moz-do-not-send="true">
https://github.com/jhpoelen/globis-b-interactions/blob/master/text/on-species-interaction-data-models-and-formats.md</a>
.
<span style="color:#1F497D"><o:p></o:p></span></p>
<p><span style="color:#1F497D">---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.<o:p></o:p></span></p>
<p>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).
<o:p></o:p></p>
<p><span style="color:#1F497D">---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.<o:p></o:p></span></p>
<p>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.
<o:p></o:p></p>
<p><span style="color:#1F497D">---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.</span><o:p></o:p></p>
<p>Do you have some samples that you can share so that I can get
a sense of what you currently have?
<o:p></o:p></p>
<p><span style="color:#1F497D">---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).<o:p></o:p></span></p>
<p><span style="color:#1F497D">---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?<o:p></o:p></span></p>
<p><span style="color:#1F497D">Cheers,<o:p></o:p></span></p>
<p><span style="color:#1F497D">John</span><o:p></o:p></p>
<p>thx,<o:p></o:p></p>
<p>-jorrit<o:p></o:p></p>
<p><a
href="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="
moz-do-not-send="true">https://globalbioticinteractions.org</a>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/19/18 6:21 PM, Bates, Robert P
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi John,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><a
href="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="
moz-do-not-send="true">http://www.obofoundry.org/ontology/ro.html</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">-R<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal"><b><span style="font-size:14.0pt">Robert
Bates</span></b><o:p></o:p></p>
<p class="MsoNormal">Research Scientist<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Design & Intelligence Lab<o:p></o:p></p>
<p class="MsoNormal"><b>Georgia Institute of Technology</b><o:p></o:p></p>
<p class="MsoNormal">Technology Square Research Building, 85
5th Street NW, Atlanta, GA 30308<o:p></o:p></p>
<p class="MsoNormal">e: <a href="mailto:rbates8@gatech.edu"
moz-do-not-send="true"><span style="color:purple">rbates8@gatech.edu</span></a><o:p></o:p></p>
<p class="MsoNormal">m: 770.713.8531<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt">From:
</span></b><span style="font-size:12.0pt">GloBI
</span><a href="mailto:globi-bounces@lists.gbif.org"
moz-do-not-send="true"><span style="font-size:12.0pt"><globi-bounces@lists.gbif.org></span></a><span
style="font-size:12.0pt"> on behalf of John Oswald
</span><a href="mailto:j-oswald@tamu.edu"
moz-do-not-send="true"><span style="font-size:12.0pt"><j-oswald@tamu.edu></span></a><span
style="font-size:12.0pt"><br>
<b>Date: </b>Monday, November 19, 2018 at 9:18 PM<br>
<b>To: </b></span><a href="mailto:globi@lists.gbif.org"
moz-do-not-send="true"><span style="font-size:12.0pt">"globi@lists.gbif.org"</span></a><span
style="font-size:12.0pt">
</span><a href="mailto:globi@lists.gbif.org"
moz-do-not-send="true"><span style="font-size:12.0pt"><globi@lists.gbif.org></span></a><span
style="font-size:12.0pt"><br>
<b>Subject: </b>[GloBI] Ontology of Biotic
Interactions?</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">---oo0oo---<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">John D. Oswald<o:p></o:p></p>
<p class="MsoNormal">Professor of Entomology<o:p></o:p></p>
<p class="MsoNormal">Curator, Texas A&M University Insect
Collection<o:p></o:p></p>
<p class="MsoNormal">Department of Entomology<o:p></o:p></p>
<p class="MsoNormal">Texas A&M University<o:p></o:p></p>
<p class="MsoNormal">College Station, TX 77843-2475<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">E-mail: <a
href="mailto:j-oswald@tamu.edu" moz-do-not-send="true"><span
style="color:blue">j-oswald@tamu.edu</span></a><o:p></o:p></p>
<p class="MsoNormal">Phone: 1-979-862-3507<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Lacewing Digital Library: <a
href="http://lacewing.tamu.edu/" moz-do-not-send="true">
<span style="color:blue">http://lacewing.tamu.edu/</span></a><o:p></o:p></p>
<p class="MsoNormal">Bibliography of the Neuropterida: <a
href="http://lacewing.tamu.edu/Biblio/Main"
moz-do-not-send="true">
<span style="color:blue">http://lacewing.tamu.edu/Biblio/Main</span></a><o:p></o:p></p>
<p class="MsoNormal">Neuropterida Species of the World: <a
href="http://lacewing.tamu.edu/SpeciesCatalog/Main"
moz-do-not-send="true">
<span style="color:blue">http://lacewing.tamu.edu/SpeciesCatalog/Main</span></a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>GloBI mailing list<o:p></o:p></pre>
<pre><a href="mailto:GloBI@lists.gbif.org" moz-do-not-send="true">GloBI@lists.gbif.org</a><o:p></o:p></pre>
<pre><a href="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=" moz-do-not-send="true">https://lists.gbif.org/mailman/listinfo/globi</a><o:p></o:p></pre>
</blockquote>
</div>
</blockquote>
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