Following on from earlier posts on annotating biodiversity data (Rethinking annotating biodiversity data and More on annotating biodiversity data: beyond sticky notes and wikis) I've started playing with user interfaces for editing data.

Following on from the previous post Rethinking annotating biodiversity data, here are some more thoughts on annotating biodiversity data. Annotations as sticky notes I get the sense that most people think of annotations as "sticky notes" that someone puts on data. In other words, the data is owned by somebody, and anyone who isn't the owner gets to make comments, which the owner is free to use or ignore as they see fit.

TL;DR By using bookmarklets and a central annotation store, we can build a system to annotate any biodiversity database, and display those annotations on those databases.A couple of weeks ago I was at GBIF meeting in Copenhagen, and there was a discussion about adding a new feature to the GBIF portal. The conversation went something like this: Resources are limited, and adding new features to a project can be difficult.

Europe PMC has added protein and chemical structures from Protein Data Bank (PDB) and ChEBI via the BioEntities tab.

VertNet has announced that they have implemented issue tracking using GitHub. This is a really interesting development, as figuring out how to capture and make use of annotations in biodiversity databases is a problem that's attracting a lot of attention.

Given that it's the start of a new year, and I have a short window before teaching kicks off in earnest (and I have to revise my phyloinformatics course) I'm playing with a few GBIF-related ideas. One topic which comes up a lot is annotating and correcting errors. There has been some work in this area [1][2] bit it strikes me as somewhat complicated.

A Grassroots Funding effort in Puerto Rico enables genome sequencing of the critically endangered Puerto Rican parrot The rationale and scope for GigaScience has been to cover and provide a home for the growing number of studies producing and handling large-scale biological data, and this “big-data” data bonanza is not just due to well funded labs, but an increasingly globalized and distributed network of researchers.

tl;dr Readmill might be a great platform for shared annotation and correction of Biodiversity Heritage Library content.Thinking about accessing the taxonomic literature I started revisiting previous ideas.

Type any scientific term into any search engine and its pretty much guaranteed that a Wikipedia article will be the first hit.

One reason I'm pursuing the theme of specimen identifiers (and identifiers in general) is the central role they play in annotating databases. To give a concrete example, I (among others) have argued for a wiki-style annotation layer on top of GenBank to capture things such as sequencing errors, updated species names, etc. Annotation is a lot easier if we have consistent identifiers for the things being annotated.