openfda

shing linked research that's reproducible (#LinkedResearch, #LinkedReproducibility) is a worthwhile investment in meta-research that we have barely yet addressed: > http://Schema.org/NewsArticle .citation: https://schema.org/citation ... Wouldn't it be great if NewsArticles linked to the ScholarlyArticle and/or Notebook CreativeWorks that they're .about (with reified relations)? > A practical use case: Alice wants to publish a ScholarlyArticle [1] (in HTML with structured data, as a PDF) predicated upon Datasets [2] (as CSV, CSVW JSONLD, XLSX (DataDownload)) with static HTML (and no special HTTP headers). 1 https://schema.org/ScholarlyArticle 2 https://schema.org/Dataset* > B wants to build a meta analysis: to collect a # of ScholarlyArticles and Dataset DataDownloads; review study controls and data; merge, join, & concatenate Datasets if appropriate, and inductively or deductively infer a conclusion and suggestions for further studies of variance* The Linked Open Data Cloud shows the edges, the relations, the structured data links between very many (life sciences) datasets: https://lod-cloud.net/ . https://5stardata.info/en/ lists TimBL's suggested 5-start deployment schema for Open Data; which culuminates in publishing linked open data in non-proprietary formats that uses URIs to describe and link to things. Could any of these [1][2][3][4][5] services cross-link the described resources, given a common URI identifier such as https://schema.org/identifier and/or https://schema.org/url ? ORCID is a service for generating stable identifiers for researchers and publishers who have names in common but different emails. W3C DID solves for this need in a different way. When I check an article result page with the OpenLink OSDS extension (or any of a number of other tools for extracting structured data from HTML pages (and documents!) https://github.com/CodeForAntarctica/codeforantarctica.githu... ), there could be quite a bit more data there for search engines, browser extensions, and meta-research tools. Is this something like ElasticSearch on the backend? It is possible to store JSON-LD documents in the search index. I threw together elasticsearchjsonld to "Generate JSON-LD @contexts from ElasticSearch JSON Mappings" for the OpenFDA FAERS data a few year ago. That's not GraphQL or SPARQL, but it's something and it's Linked Data. re: "Canada's Decision To Make Public More Clinical Trial Data Puts Pressure On FDA" https://news.ycombinator.com/item?id=21232183 > We really could get more out of this data through international collaboration and through linked data (e.g. URIs for columns). See: "Open, and Linked, FDA data" https://github.com/FDA/openfda/issues/5#issuecomment-5392966... and "ENH: Adverse Event Count / 'Use' Count Heatmap" https://github.com/FDA/openfda/issues/49 . With sales/usage counts, we'd have a denominator with which we could calculate relative hazard. W3C Web Annotations handle threaded comments and highlights; reviewing the reviewers is left as an exercise for the reader. Does Zotero still make it easy to save the bibliographic metadata for one or more ScholarlyArticles from PubMed to a collection in the cloud (and add metadata/annotations)? Sorry to toot my own horn here. Great job on this. This opens up many new opportunities for research. [1] https://scholar.google.com [2] https://www.semanticscholar.org/ [3] https://www.meta.org/ [4] https://zotero.org/ [5] https://mendeley.org/

to parse/scrape their sites. (FDA has always had really exhaustive dumps of their data...strewn about their legacy site...the API isn't as interesting to me as the documentation for the API and the pipeline of data) * I don't want to just slag on Drupal...but Drupal was what Obama's head tech officer wanted in place, and to their credit, they did open-source parts of their custom Drupal modules...which were not particularly useful, because of the particulars of Drupal's module system and its quickly changing API...nevermind being only useful for other Drupal installations. But a lot of credit has to go to the U.S. gov't for pivoting off of Drupal to a mix of WordPress, Jekyll, and even node.js sites with less coupled components. It's been only about two or so years since Data.gov open-sourced its Drupal components before promptly switching to WordPress and CKAN modules...considering how a non-significant number of the fed sites are built on 12+ year-old code...the turnaround in the U.S. gov's stack is pretty amazing...(when it's not attempted on a service-critical site, such as healthcare.gov)