University of Glasgow

Roderic Page

> Let's rise up to unite taxonomy and technology - I thought it already
> was? [@rdmpage](https://twitter.com/rdmpage) <https://t.co/AkNz1GYGbw>
>
> --- Sjúrður Hammer 🐣 (@sjurdur) [August 26,
> 2017](https://twitter.com/sjurdur/status/901460750513950720)

Holly Bik ([@hollybik](https://twitter.com/hollybik)) has an opinion
piece in PLoS Biology entitled \"Let's rise up to unite taxonomy and
technology\" <https://doi.org/10.1371/journal.pbio.2002231> (thanks to
[@sjurdur](https://twitter.com/sjurdur) for bringing this to my
attention).

![Journal pbio 2002231
g001](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4h-iURv-SJ_NySgB30d-4tTE4uYwZPHqgVli2VP2Z4z2TZVUkrzMILTJtAn_lBQMFAclckgGpCN1bTJdvo63I8x9UOOMGDsa350dCHMy9uM4RhZ3VE4EP6WxbFPsAD729Qw6_/?imgmax=1600 "journal.pbio.2002231.g001.PNG"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="100%"}

It\'s a passionate plea for integrating taxonomic knowledge and
\"omics\" data. In her article Bik includes a mockup of the kind of tool
she\'d like to see (based in part on [Phinch](http://phinch.org)), and
writes:

> Step 2: Clicking on a specific data point (e.g., an OTU) will pull up
> any online information associated with that species ID or taxonomic
> group, such as Wikipedia entries, photos, DNA sequences, peer-reviewed
> articles, and geolocated species observations displayed on a map.

This sort of plea has been made any times, and reminds me very much of
PLoS\'s own efforts when they wanted to build a \"Biodiversity Hub\" and
biodiversity informatics basically [failed
them](http://iphylo.blogspot.com/2010/04/biodiversity-informatic-fail-and-what.html).
The hub itself later [closed
down.](http://iphylo.blogspot.com/2013/07/the-demise-of-plos-biodiversity-hub.html).
There\'s clearly a need for a simply way to summarise what we know about
a species, but we\'ve yet to really tackle this (on the face of it)
fairly simple task.

Quickly summarising the available information about a species was the
motivation behind my little tool [iSpecies](http://ispecies.org), which
I recently reworked to use DBpedia, GBIF, CrossRef, EOL, TreeBASE and
OpenTreeofLife as sources. For the nematode featured in Bik\'s figure
(*Desmoscolex*) there\'s not a great deal of easily available
information (see <http://ispecies.org/?q=Desmoscolex>). We can get a
little more form other sources not queried by iSpecies, such as
BioNames, which aggregates the primary taxonomic literature, see
<http://bionames.org/search/Desmoscolex>.

Part of the problem is that taxonomy is fundamentally a \"long tail\"
field, both in terms of the subject matter (a few very well know
species, then millions of poorly known species) and our knowledge of
those species (a large, scattered taxonomic literature, much of it not
yet digitised, although progress is being made). Furthermore, the names
of species (and our conception of them) can change, adding an additional
challenge.

But I think we can do a lot better. Simple web-based tools like iSpecies
can assemble reasonable information from multiple sources (and in
multiple languages) on the fly. It would be nice to expand those sources
(the more primary sources the better). The current iSpecies tool
searches on species name. This works well if the sources being queried
mention that name (e.g., in the title of a paper that has a DOI and is
indexed by CrossRef). Given that many of the \"omics\" datasets Bik
works with are likely to have [dark
taxa](http://iphylo.blogspot.com/2011/04/dark-taxa-genbank-in-post-taxonomic.html),
what we\'ll also need is the ability to search, say, using NCBI taxon
ids, and retrieve literature linked to sequences for those taxa

It would also be useful to package those up in a simple API that other
tools could consume. For example, if I wanted to improve the utility of
iSpecies, one approach would be to package up the results in a JSON
object. Perhaps even use JSON-LD (with global identifiers for taxa,
documents, etc.) to make it possible for consumers to easily integrate
that data with their own.

> Taxonomy could be on the brink of another golden age---if we play our
> cards right. As it is reinvented and reborn in the 21st century,
> taxonomy needs to retain its traditional organismal-focused approaches
> while simultaneously building bridges with phylogenetics, ecology,
> genomics, and the computational sciences.

Taxonomy is, of course, doing just this, albeit not nearly fast enough.
There are some pretty serious obstacles, some of them cultural, but some
of them due to the nature of the problem. Taxonomic knowledge is
massively decentralised, mostly non-digital, and many of the key sources
and aggregations are behind paywalls. There is also a fairly large
\"[technical debt](https://en.wikipedia.org/wiki/Technical_debt)\" to
deal with. Ian Mulvany was recently interviewed by PLoS and he
emphasised that because academic publishers had been online from early
on they were pioneers, but at the same time this left them with a legacy
of older technologies and approaches that can sometimes get in the way
of new idea. I think taxonomy suffers from some of the same problems.
Because taxonomy has long been involved with computers, sometime we
needed up betting on the \"wrong\" solutions. For example, at one time
XML was the new hotness, and people invested a lot of effort in
developing XML schema, and then ontologies and RDF vocabularies.
Meantime much of the web has moved to simple data formats such as JSON,
many specialist vocabularies are gathering dust as
[schema.org](http://schema.org) takes off, and projects like Wikidata
force us to rethink the need to topic-specific databases.

But these are technical details. For me the key point of \"Let's rise up
to unite taxonomy and technology\" is that it\'s a symptom of the
continued failure of biodiversity informatics to actually address the
needs of its users. People keep asking for fairly simple things, and we
keep ignoring them (or explaining why it\'s MUCH harder than people
think, which is another way of ignoring them).

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Holly Bik (@hollybik) has an opinion piece in PLoS Biology entitled "Let’s rise up to unite taxonomy and technology" https://doi.org/10.1371/journal.pbio.2002231 (thanks to @sjurdur for bringing this to my attention).    It's a passionate plea for integrating taxonomic knowledge and "omics" data.

Messaggi di Rogue Scholar

Let’s rise up to unite taxonomy and technology