Some notes on containers, microservices, and data. The idea of packaging software into portable containers and running them either locally or in the cloud is very attractive (see Docker). Some use cases I'm interested in exploring.
I've been experimenting with simple spatial search in BioStor, as shown in the demo below. If you go to the map on BioStor you can use the tools on the left to draw a box or a polygon on the map, and BioStor will search it's database for articles that mention localities that occur in that region. If you click on a marker you can see the title of the article, clicking on that title takes you to the article itself.
In between complaining about the lack of open data in biodiversity (especially taxonomy), and scraping data from various web sites to build stuff I'm interested in, I occasionally end up having interesting conversations with the people whose data I've been scraping, cleaning, cross-linking, and otherwise messing with. Yesterday I had one of those conversations at Kew Gardens.
In the previous post I sketched out a workflow to annotate articles using hypothes.is and aggregate those annotations.
I will be at ReCon 16 in Edinburgh (hashtag #ReCon_16), the second ReCon event I've attended (see Thoughts on ReCon 15: DOIs, GitHub, ORCID, altmetric, and transitive credit). For the hack day that follows I've put together some instructions for a way to glue together annotations made by multiple people using hypothes.is. It works by using IFTTT to read a user's annotation stream (i.e., the annotations they've made) and then post those to a
The last few days I've been re-reading articles about Ted Nelson's work (including ill-fated Project Xanadu), reading articles celebrating his work (brought together in the open access book "Intertwingled"), playing with Hypothes.is, and thinking about annotation and linking.
Given that Wikipedia, Wikidata, and the Biodiversity Heritage Library (BHL) all share the goal of making information free, open, and accessible, there seems to be a lot of potential for useful collaboration. Below I sketch out some ideas. BHL as a source of references for Wikipedia Wikipedia likes to have sources cited to support claims in its articles. BHL has a lot of articles that could be cited by Wikipedia articles.
I'll be taking a break shortly, so I thought I'd try to gather some thoughts on a few projects/ideas that I'm working on. These are essentially extended notes to myself to jog my memory when I return to these topics. BOLD data into GBIF Following on from work on getting mosquito data into GBIF I've been looking at DNA barcoding data. BOLD data is mostly absent from GBIF.
Awoke this morning to the sad news (via Scott Miller) that Scott Federhen of the NCBI had died. Anyone using the NCBI taxonomy is a beneficiary of Scott's work on bring together taxonomy and genomic data. Scott contributed both directly and indirectly to this blog.
Some notes to self about future directions for the "million DNA barcodes map" http://iphylo.org/~rpage/bold-map/. At the moment we have an interactive map that we can pan and zoom, and click on a marker to get a list of one or more barcodes at the location. We can also filter by major taxonomic group. Here are some ideas on what could be next. Search At the moment search is simply browsing the map.
Kew has released a new report today, entitled the State of the World's Plants, complete with it's own web site https://stateoftheworldsplants.com. Its aim: This is, of course, a laudable goal, and a lot of work has gone into this report, and yet there are some things about the report that I find very frustrating.