Exploring the OpenAlex Data Structure and Visualization Author: Qingqin Fang ( ORCID: 0009–0003–5348–4264) Introduction to OpenAlex In today’s world, the realm of research papers is brimming with countless hot topics, and the sheer volume of publications can be overwhelming.

Plants are full of biochemical potential. Today in GigaScience, we publish an article that presents a searchable library of spectra and molecules found in a collection of 1,600 plant extracts.

\ Code is often arranged in packages for any given language. Packages are often cataloged in a package registry of some kind: NPM for node, crates.io for Rust, etc. For R, that registry is either CRAN or Bioconductor (for the most part). CRAN has the concept of an archived package.

taxizedb arose from pain in using taxize when dealing with large amounts of data in a single request or doing a lot of requests of any data size. taxize works with remote data sources on the web, so there’s a number of issues that can slow the response down: internet speed, server response speed (was a response already cached or not; or do they even use caching), etc.

FAIRer Sharing via FAIRsharing Image from FAIRsharing.org. Our aim at GigaScience is to provide the means to open up and share research data. On top of just making these available via our (new look) GigaDB database, we’ve been involved with communities that wants to maximize the utility of these research outputs by making them FAIR: Findable, Accessible, Interoperable and Reusable.

Quick notes on modelling taxonomic names in databases, as part of an ongoing discussion elsewhere about this topic. Simple model One model that is widely used (e.g., ITIS, WoRMS) and which is explicit in Darwin Core Archive is something like this: We have a table for taxa and we don't distinguish between taxa and their names. the taxonomic hierarchy is represented by the parentID field, which points to your parent.

Endorsing Data Citation Nicely timed for the Data Citation Principles workshop at the IDCC meeting in San Francisco yesterday, the finalized Joint Declaration of Data Citation Principles has just been posted on the Force11 website.

Yet another taxonomic database, this time I can't blame anyone else because I'm the one building it (with some help, as I'll explain below).BioNames was my entry in EOL's Computable Data Challenge (you can see the proposal here: http://dx.doi.org/10.6084/m9.figshare.92091). In that proposal I outlined my goal:The bulk of the funding from EOL is going into interface work by Ryan Schenk (@ryanschenk), author of synynyms among other cool things.

It is well known that phylogeny databases such as TreeBASE capture a small fraction of the published phylogenies. This raises the question of how to increase the number of trees that get archived.

This post was prompted by Stephen Thorpe's post on TAXACOM about Wikispecies in which he wrote (in a thread discussing Roger Hyam's recent blog post) thatI beg to differ. Wikispecies runs on a database (the Mediawiki software uses a database to store the wiki), and Mediawiki can be thought of as a database of semi-structured text, but it lacks a lot of the functionality database users would expect.