Wednesday, May 09, 2018

World Taxonomists and Systematists via ORCID

Taxonomist mapDavid Shorthouse (@dpsspiders) makes some very cool things, and his latest project World Taxonomists & Systematists is a great example of using automation to assemble a list of the world's taxonomists and systematists. The project uses ORCID. As many researchers will know, ORCID's goal is to have every researcher uniquely identified by an ORCID id (mine is that is linked to all a researcher's academic output, including papers, datasets, and more. So David has been querying ORCID for keywords such as taxonomist, taxonomy, nomenclature, or systematics to locate taxonomists and add them to his list. For more detail see his post on the ORCID blog.

Using ORCIDs to help taxonomists gain visibility is an idea that's been a round for a little while. I blogged about it in Possible project: #itaxonomist, combining taxonomic names, DOIs, and ORCID to measure taxonomic impact, at which time David was already doing another cool piece of work linking collectors to ORCIDs and their collecting effort, see e.g. data for Terry A. Wheeler.

There are, of course, a bunch of obstacles to this approach. Many taxonomists lack ORCIDs, and I keep coming across "private" ORCIDs where taxonomists have an ORCID id but don't make their profile public, which makes it hard to identify them as taxonomists. Typically I discover these profiles via metadata in CrossRef, which will list the ORCID id for any authors that have them and have made them know to the publisher of their paper.

ORCID ids are only available for people who are alive (or alive recently enough to have registered), so there will be many taxonomists who will never have an ORCID id. In this case, it may be Wikidata to the rescue:

Many taxonomists have Wikidata entries because they are either notable enough to be in Wikipedia, or they have an entry in Wikispecies, and people like Andy Mabbett (@pigsonthewing) have been diligently ensuring these people have Wikidata entries. There's huge scope for making use of these links.

Meanwhile, if you are a taxonomist or a systematist and you don't have an ORCID, get yourself one at ORCID, claim your papers, and you should appear shortly in the World Taxonomists & Systematists list.

2018 GBIF Ebbe Nielsen Challenge now open

Http images ctfassets net uo17ejk9rkwj L6lRFOvdQG4M4yY0k0Cei ad53f85a57368b017fecb8907393d32a ebbe 2018Last year I finished my four-year stint as Chair of the GBIF Science Committee. During that time, partly as a result of my urging, GBIF launched an annual "GBIF Ebbe Nielsen Challenge", and I'm please that this year GBIF is continuing to run the challenge. In 2015 and 2016 the challenge received some great entries.

Last year's challenge (GBIF Challenge 2017: Liberating species records from open data repositories for scientific discovery and reuse didn't attract quite the same degree of attention, and GBIF quietly didn't make an award. I think part of the problem was that there's a fine balance between having a wide open challenge which attracts all sorts of interesting entries, some a little off the wall (my favourite was GBIF data converted to 3D plastic prints for physical data visualisation) versus a specific topic which might yield one or more tools that could, say, be integrated into the GBIF portal. But if you make it too narrow then you run the risk of getting fewer entries, which is what happened in 2017. Ironically, since the 2017 challenge I've come across work that would have made a great entry, such as a thesis by Ivelize Rocha Bernardo Promoting Interoperability of Biodiversity Spreadsheets via. Purpose Recognition, see also Bernardo, I. R., Borges, M., Baranauskas, M. C. C., & Santanchè, A. (2015). Interpretation of Construction Patterns for Biodiversity Spreadsheets. Lecture Notes in Business Information Processing, 397–414. doi:10.1007/978-3-319-22348-3_22.

This year the topic is pretty open:

The 2018 Challenge will award €34,000 for advancements in open science that feature tools and techniques that improve the access, utility or quality of GBIF-mediated data. Under this open-ended call, challenge submissions may build on existing tools and features, such as the GBIF API, Integrated Publishing Toolkit, data validator, relative species occurrence tool, among others—or develop new applications, methods, workflows or analyses.

Lots of scope, and since I'm not longer part of the GBIF Science Committee it's tempting to think about taking part. The judging criteria are pretty tough and results-oriented:

Winning entries will demonstrably extend and increase the usefulness, openness and visibility of GBIF-mediated data for identified stakeholder groups. Each submission is expected to demonstrate advantages for at least three of the following groups: researchers, policymakers, educators, students and citizen scientists.

So, maybe less scope for off-the-wall stuff, but an incentive to clearly articulate why a submission matters.

The actual submission process is, sadly, rather more opaque than in previous years where it was run in the open on Devpost where you can still see previous submissions (e.g., those for 2015). Devpost has lots of great features but isn't cheap, so the decision is understandable. Maybe some participants will keep the rest of the community informed via, say, Twitter, or perhaps people will keep things close to their chest. In any event, I hope the 2018 challenge inspires people to think about doing something both cool and useful with biodiversity data. Oh, and did I mention that a total of €34,000 in prizes is up for grabs? Deadline for submission is 5 September 2018.

iSpecies meets Lifemap

It's been a little quiet on this blog as I've been teaching, and spending a lot of time data wrangling and trying to get my head around "data lakes" and "triple stores". So there are a few things to catch up on, and a few side projects to report on.

I continue to play with iSpecies, which is a simple mashup off biodiversity data sources. When I last blogged about iSpecies I'd added TreeBASE as a source (iSpecies meets TreeBASE). iSpecies also queries Open Tree of Life, and I've always wanted a better way of displaying the phylogenetic context of a species or genus. TreeBASE is great for a detailed, data-driven view, but doesn't put the taxon in a larger context, nor does the simple visualisation I developed for Open Tree of Life.

A nice large-scale tree visualisation is Lifemap (see De Vienne, D. M. (2016). Lifemap: Exploring the Entire Tree of Life. PLOS Biology, 14(12), e2001624. doi:10.1371/journal.pbio.2001624), and it dawned on me that since Lifemap uses the same toolkit (leaflet.js) that I use to display a map of GBIF records, I could easily add it to iSpecies. After looking at the Lifemap HTML I figured out the API call I need to pan the map to given taxon using Open Tree of Life taxon identifiers, and violà, I now have a global tree of life that shows where the query taxon fits in that tree.

Here's a screenshot of a search for Podocarpus showing the first 300 records from GBIF, and the position of Podocarpus in the tree of life. The tree is interactive so you can zoom and pan just like the GBIF map.

Screenshot 2018 05 09 16 58 00

Here's another one for the genus Timonius:

Screenshot 2018 05 09 17 58 32

Very much still at the "quick and dirty" stage, but I continue to marvel at how much information can be assembled "on the fly" from a few sources, and how much richer this seems than what biodiversity informatics projects offer. There's a huge amount of information that is simpy being missed or under-utilised in this area.