Jorrit Poelen

Jorrit Poelen
Research Scholar
Biodiversity Informatics
This user account status is Approved

This user has not added any information to their profile yet.

My goal is to help realize Charles
Elton's dream to "link up into some complete scheme the colossal store of
facts about natural history" (Elton 1927 [3]) to enable biodiversity
research and better understand the natural world around us.

I use my software engineering skills
to develop new methods to solve "impossible" integration problems in
biodiversity informatics. I use, or build, open source software to integrate,
and study, open biodiversity data.

After spending about a decade in
industry, I was re-introduced to academia in 2011 by attending the Ecological
Integration Symposium at Texas A&M College Station. As an invited visual
artist, I was asked to take a minute or two to introduce my video installation
“Evidence of Use” to the conference attendees. I noticed the audience freeze
when I suggested that all scientific data should be liberated for the
unrestricted enjoyment of scientists and artists alike. Fortunately, after the
talk, I was approached by an enthousiastic audience member who introduced me to
his big dream and his excel spreadsheet with fish stomach diet data. This
marked my unlikely entry into the field of ecological informatics and the start
of my collaboration with Jim Simons, then marine biologist at Texas A&M
Corpus Christi. Our complementary skills and shared enthusiasm led to the
materialization of the Gulf of Mexico Species Interactions (GoMexSI, [1]) and
Global Biotic Interactions (GloBI,
[2]) projects. Both projects re-purpose existing species datasets in an attempt
to realize Charles Elton’s vision to “[...] provide conceptions which can link
up into some complete scheme the colossal store of facts about natural history
[...]” ([3]).  GoMexSI focus is on synthesis
of marine food webs in the Gulf of Mexico, while GloBI aims to make it easier
to share and find any openly available species interaction (e.g.,
parasite-host, plant-pollinator, predator-prey) claim.

As a small, independent, open
source and open data developer, I have no choice but to make use of openly
available datasets, leverage cheap (or open) compute infrastructures, and
establish a wide range of mutually beneficial research collaborations with
institutional scientists.  I have noticed
that my frugal approach to software design, automation and collaborations have
resulting in a sustained, economically viable, way of life with beneficial side
effects such as:

1. Providing a de-facto continuous
peer-review service of existing open datasets and -services ([4]).

2. Developing pragmatic approaches
to link biological data at scale ([5], [6]).

3. Engaging in, and enabling of,
“risky” scientific studies that re-use existing datasets to answer (global)
questions ([7], [8]).

4. Catalyzing discussions around
data integration, frugal tools, data preservation, data standards and
ontologies ([9], [10], [11]).

Over the years, I have come to
realize that many of my contributions to the academic community cannot be
measured in, or are often detrimental to, traditional metrics like citation
indexes, grant moneys, institutional affiliation, and academic tenure. With
this, I would like to think that, as a free-living parasite/ symbiont, I help
my hosts evolve by transferring infectious new ideas across disciplinary and
institutional boundaries.

You can reach me via jorrit.poelen at ronininstitute dot org . For more information, please see .


[1] Simons JD, Yuan M, Carollo C, Vega-Cendejas M, Shirley T,
Palomares ML, Roopnarine P,  Gerardo
Abarca Arenas L., Ibañez A. , Holmes J, Mazza Schoonard C, Hertog R, Reed D,
and Poelen JH. 2013. Building a Fisheries Trophic Interaction Database
for Management and Modeling Research in the Gulf of Mexico Large Marine
Ecosystem. Bulletin of Marine Science; Jan 1;89(1):135–60.

[2]  Poelen JH,
Simons JD, Mungall CJ. 2014. Global biotic interactions: An open infrastructure
to share and analyze species-interaction datasets. Ecological Informatics.
Nov;24:148–59. Available from:

[3] Elton CS. 1927. Animal Ecology.

[4] Poelen JH, et al. 2019 . GloBI GitHub Issues Archive
2013-2019 . GitHub.
accessed at 2019-10-14 .

[5] Thessen AE, Poelen JH, Collins M, Hammock J. 2018.
20 GB in 10 minutes: a case for linking major biodiversity databases using an
open socio-technical infrastructure and a pragmatic, cross-institutional
collaboration. PeerJ Computer Science 4:e164

[6] Grüss A, Palomares MLD, Poelen JH, Barile JR,
Aldemita CD, Ortiz SR, et al. 2019 Building bridges between global information
systems on marine organisms and ecosystem models. Ecological Modelling.

[7] Hayden B, Palomares MLD, Smith BE, Poelen JH.
2019. Biological and environmental drivers of trophic ecology in marine fishes
- a global perspective. Sci Rep. Aug 6;9(1):11415.

[8] Olivier, P. et al., 2019. Exploring the temporal
variability of a food web using long?term biomonitoring data. Ecography.
Available at:

[9] Pauli JN, Newsome SD, Cook JA, Harrod C, Steffan SA,
Baker CJO, … Poelen JH …  2017.
Opinion: Why we need a centralized repository for isotopic data. Proceedings of
the National Academy of Sciences [Internet]. Proceedings of the National
Academy of Sciences; Mar 21;114(12):2997–3001. Available from:

[10] Hardisty AR, Michener WK, Agosti D, Alonso García E,
Bastin L, Belbin L, … Poelen JH ... 2019.  The Bari Manifesto: An interoperability
framework for essential biodiversity variables. Ecological Informatics.
Jan;49:22–31. Available from:

[11] Gallagher, R., Falster, D. S., Maitner, B.,
Salguero-Gomez, R., Vandvik, V., Pearse, W., … Poelen JH ... Enquist, B.
2019. The Open Traits Network: Using Open Science principles to accelerate
trait-based science across the Tree of Life. Pre-print.

Computer Science