Friday, October 06, 2017

Notes on finding georeferenced sequences in GenBank

Notes on how many georeferenced DNA sequences there are in GenBank, and how many could potentially be georeferenced.

BCT	Bacterial sequences
PRI	Primate sequences
ROD	Rodent sequences
MAM	Other mammalian sequences
VRT	Other vertebrate sequences
INV	Invertebrate sequences
PLN	Plant and Fungal sequences
VRL	Viral sequences
PHG	Phage sequences
RNA	Structural RNA sequences
SYN	Synthetic and chimeric sequ
UNA	Unannotated sequences
?db=nucleotide nucleotides
&term=ddbj embl genbank with limits[filt]
NOT transcriptome[All Fields] ignore transcriptome data
NOT mRNA[filt] ignore mRNA data
NOT TSA[All Fields] ignore TSA
NOT scaffold[All Fields] ignore scaffold
AND src lat lon[prop] include records that have source feature "lat_lon"
AND 2010/01/01:2010/12/31[pdat] from this date range
AND gbdiv_pri[PROP] restrict search to PRI division (primates)
AND srcdb_genbank[PROP] Need this if we query by division, see NBK49540

Numbers of nucleotide sequences that have latitude and longitudes in GenBank for each year.


Numbers of nucleotide sequences that don't have latitude and longitudes in GenBank for each year but do have the country field and hence could be georeferenced.


Wednesday, October 04, 2017

TDWG 2017: thoughts on day 3

Day three of TDWG 2017 highlighted some of the key obstacles facing biodiversity informatics.

After a fun series of "wild ideas" (nobody will easily forget David Bloom's "Kill your Darwin Core darlings") we had a wonderful keynote by Javier de la Torre (@jatorre) entitled "Everything happens somewhere, multiple times". Javier is CEO and founder of Carto, which provides tools for amazing geographic visualisations. Javier provided some pithy observations on standards, particularly the fate of official versus unofficial "community" standards (the community standards tend to be simpler, easier to use, and hence win out), and the potentially stifling effects standards can have on innovation, especially if conforming to standards becomes the goal rather than merely a feature.

The session Using Big Data Techniques to Cross Dataset Boundaries - Integration and Analysis of Multiple Datasets demonstrated the great range of things people want to do with data, but made little progress on integration. It still strikes me as bizarre that we haven't made much progress on minting and reusing identifiers for the same entities that we keep referring too. Channeling Steve Balmer:

Identifiers, identifiers, identifiers, identifiers

It's also striking to compare Javier de la Torre's work with Carto where there is a clear customer-driven focus (we need these tools to deliver this to users so that they can do what they want to do) versus the much less focussed approach of our community. Many of the things we aspire to won't happen until we identify some clear benefits for actual users. There's a tendency to build stuff for our own purposes (e.g., pretty much everything I do) or build stuff that we think people might/should want, but very little building stuff that people actually need.

TDWG also has something of an institutional memory problem. Franck Michel gave an elegant talk entitled A Reference Thesaurus for Biodiversity on the Web of Linked Data which discussed how the Muséum national d'Histoire naturelle's taxonomic database could be modelled in RDF (see for example There's a more detailed description of this work here:

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What struck me was how similar this was to the now deprecated TDWG LSID vocabulary, still used my most of the major taxonomic name databases (the nomenclatures). This is an instance where TDWG had a nice, workable solution, it lapsed into oblivion, only to be subsequently reinvented. This isn't to take anything away from Frank's work, which has a thorough discussion of the issues, and has a nice way to handle the the difference between asserting that two taxa are the same (owl:equivalentClass) and that a taxon/name hybrid (which is what many databases serve up because they don't distinguish between names and taxa) and a taxon might be the same (linking via the name they both share).

The fate of the RDF served by the nomenclators for the last decade illustrates a point I keep returning too (see also EOL Traitbank JSON-LD is broken). We tend to generate data and standards because it's the right thing to do, rather than because there's actually a demonstrable need for that data and those standards.

Bitcoin, biodiversity, and micropayments for open data

I gave a "wild ideas" talk at TDWG17 suggesting that the biodiversity community use Bitcoin to make micropayments to use data.

The argument runs like this:

  1. We like open data because it's free and it makes it easy to innovate, but we struggle to (a) get it funded and (b) it's hard to demonstrate value (hence pleas for credit/attribution, and begging for funding).
  2. The alternative of closed data, such as paying a subscription to access a database limits access and hence use and innovation, but generates an income to support the database, and the value of the database is easy to measure (it's how much money it generates).
  3. What if we have a "third model" where we pay small amounts of money to access data (micropayments)?

Micropayments as a way to pay creators is an old idea (it was part of Ted Nelson's Xanadu vision). Now that we have cryptocurrencies such as Bitcoin, micropayments are feasible. So we could imagine something like this:

  1. Access to raw datasets is free (you get what you pay for)
  2. Access to cleaned data comes at a cost (you are paying someone else to do the hard, tedious work of making the data usable)
  3. Micropayments are made using Bitcoin
  4. To help generate funds any spare computational capacity in the biodiversity community is used to mine Bitcoins

After the talk Dmitry Mozzherin sent me a link to Steem, and then this article about Steemit appeared in my Twitter stream:

Clearly this is an idea that has been bubbling around for a while. I think there is scope for thinking about ways to combine a degree of openness (we don't want to cripple access and innovation) with a way to fund that openness (nobody seems interested in giving us money to be open).

Tuesday, October 03, 2017

TDWG 2017: thoughts on day 1

Some random notes on the first day of TDWG 2017. First off, great organisation with the first usable conference calendar app that I've seen (

I gave the day's keynote address in the morning (slides below).

It was something of a stream of consciousness brain dump, and tried to cover a lot of (maybe too much) stuff. Among the topics I covered were Holly Bik's appeal for better links between genomic and taxonomic data, my iSpecies tool, some snarky comments on the Semantic Web (and an assertion that the reason that GenBank succeeded was due more to network effects than journals requiring authors to submit sequences there), a brief discussion of Wikidata (including using d3sparql to display classifications, see here), and the use of Hexastore to query data from BBC Wildlife. I also talked about Ted Nelson, Xanadu, using to annotate scientific papers (see Aggregating annotations on the scientific literature: a followup on the ReCon16 hackday), social factors in building knowledge graphs (touching on ORCID and some of the work by Nico Franz discussed here), and ended with some cautionary comments on the potential misuse of metrics based on knowledge graphs (using "league tables" of cited specimens, see GBIF specimens in BioStor: who are the top ten museums with citable specimens?).

TDWG is a great opportunity to find out what is going on in biodiversity informatics, and also to get a sense of where the problems are. For example, sitting through the Financial Models for Sustaining Biodiversity Informatics Products session you couldn't help being struck by (a) the number of different projects all essentially managing specimen data, and (b) the struggle they all face to obtain funding. If this was a commercial market there would be some pretty drastic consolidation happening. It also highlights the difficulty of providing services to a community that doesn't have much money.

I was also struck by Andrew Bentley's talk Interoperability, Attribution, and Value in the Web of Natural History Museum Data. In a series of slides Andrew outlined what he felt collections needed from aggregators, researchers, and publishers, e.g.:

Chatting to Andrew at the evening event at the Canadian Museum of Nature, I think there's a lot of potential for developing tools to provide collections with data on the use and impact of their collections. Text mining the biodiversity literature on a massive scale to extract (a) mentions of collections (e.g., their institutional acronyms) and (b) citations of specimens could generate metrics that would be helpful to collections. There's a great opportunity here for BHL to generate immediate value for natural history collections (many of which are also contributors to BHL).

Also had a chance to talk to Jorrit Poelen who works on Global Biotic Interactions (GloBI). He made some interesting comparisons between Hexastores (which I'd touched on in my keynote) and Linked Data Fragments.

The final session I attended was Towards robust interoperability in multi-omic approaches to biodiversity monitoring. The overwhelming impression was that there is a huge amount of genomic data, much of which does not easily fit into the classic, Linnean view of the world that characterises, say, GBIF. For most of the sequences we don't know what they are, and that might not be the most interesting question anyway (more interesting might be "what do they do?"). The extent to which these data can be shoehorned into GBIF is not clear to me, although doing so may result in some healthy rethinking of the scope of GBIF itself.