Bioschemas News

Bioschemas Resource Index for Chem and Plants

Published: 30 January 2024
Tags: NFDI FAIRAgro NFDI4Biodiversity BHEU2023 Preprint BioHackrXiv

We are pleased to announce the second BioHackrXiv preprint of 2024. It reports on the work done during the past BioHackathon Europe 2023 by the group Bioschemas resource index for chem and plants.

BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas

Published: 26 January 2024
Tags: RO-crate Signposting FDO BHEU2023 Preprint BioHackrXiv

We are pleased to announce the first BioHackrXiv preprint of 2024. It reports on the work done during the past BioHackathon Europe 2023 by the group Enabling FAIR Digital Objects with RO-Crates, Signposting and Bioschemas.

Projects Accepted at BioHackathon-Europe 2023

Published: 24 June 2023
Tags: Community Event

We are pleased to announce that the Bioschemas community have had three projects accepted at this year’s BioHackathon-Europe event beginning 30th October.

BioHackathon 2022 preprint ETL for Knowledge Graph

Published: 20 May 2023
Tags: Knowledge Graph JSON-LD SPARQL Community

We are pleased to announce, belatedly, that our preprint from BioHackathon 2022 is available here

Schema Playground publication

Published: 10 May 2023
Tags: Profile Tooling Community

We are pleased to announce that the Schema Playground publication from BMC Bioinformatics is available.

BioHackathon 2022 preprint DDE & Profiles

Published: 10 May 2023
Tags: Profile Tooling Community

We are pleased to announce that our preprint from BioHackathon 2022 is available here

ELIXIR-DE BioHackathon Wrapup

Published: 24 January 2023
Tags: Community

In December the first BioHackathon Germany was organised by the team of the German ELIXIR node. Leyla Jael Garcia-Castro (ZBMed and NFDI4Microbiota) and Steffen Neumann (IPB Halle and NFDI4Chem) used the opportunity and successfully submitted a proposal on (Bio)Schemas4NFDI.

SIB TRaining Portal Deployment of the CourseInstance Profile

Published: 17 November 2022
Tags: Deployment CourseInstance

SIB Training Portal is an online resource for training in Bioinformatics offering courses, course instances and training material to the public. SIB Training Portal uses Bioschemas training profiles to make their training resources more Findable, Accessible, Interoperable and Reusable (FAIR). In particular they are using the CourseInstance Bioschemas profile.

Steering Council Update

Published: 10 November 2022
Tags: Community

We are pleased to announce our new Steering Council

Chair: Leyla Jael Castro
Research Infrastructure Liaison: Nick Juty (Vice Chair)
Engagement and Adoption: Ivan Mičetić
Support Tools: Chunlei Wu and Alban Gaignard
Operations Manager: Ginger Tsuegn
Community Members: Dan Brickley and Carole Goble

Course and CourseInstance Profile 1.0-RELEASE Published

Published: 13 September 2022
Tags: Profile Course CourseInstance

We are pleased to announce the long-awaited release of the Course and CourseInstance profiles from the Training Working Group.

Course and CourseInstance 1.0 Request for Comments

Published: 18 August 2022
Tags: Profile Course CourseInstance RequestForComment

The Training Working Group have requested that the community consider the Course and CourseInstance profiles for release based on the Course 0.10-DRAFT and CourseInstance 0.9-DRAFT versions. The final versions are available for preview at Course 1.0-RELEASE and CourseInstance 1.0-RELEASE.
Note that relative URLs do not work correctly on the preview deployment so some links will appear broken.

Bioinformatics.ca deploys Bioschemas

Published: 22 July 2022
Tags: Deployment Course CourseInstance

Bioinformatics.ca is the home of the Canadian Bioinformatics Workshops and bioinformatics resources in Canada, and provide advanced training in bioinformatics and advanced research. To make their content more discoverable, they have added Course and CourseInstance markup to their site.

EMBL-EBI Training deploys Bioschemas

Published: 21 July 2022
Tags: Deployment Course CourseInstance

EMBL-EBI Training team provide world-class training in data-driven life sciences. They have added Course and CourseInstance markup to their site, some 300 courses, to make their training courses more discoverable both through TeSS and Google.

Dataset Profile 1.0-RELEASE Published

Published: 12 July 2022
Tags: Profile Dataset

We are pleased to announce the latest release of the Dataset profile from the Datasets Working Group. This release represents a tidying up of the profile reflecting changes that have been made in the Schema.org vocabulary.

Galaxy Training Network deploys Bioschemas

Published: 07 June 2022
Tags: Deployment Person TrainingMaterial

The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy. These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!

TrainingMaterial Profile 1.0-RELEASE Published

Published: 01 June 2022
Tags: Profile TrainingMaterial

We are pleased to announce the long-awaited release of the TrainingMaterials profile from the Training Working Group.

Three Projects Accepted at BioHackathon-Europe 2022

Published: 19 May 2022
Tags: Community Event

We are pleased to announce that the Bioschemas community have had three projects accepted at this year’s BioHackathon-Europe event taking place in November.

Dataset 1.0 Request for Comments

Published: 16 May 2022
Tags: Profile Dataset RequestForComment

The Datasets Group have requested that the community consider the updated Dataset profile for release based on the current 0.5-DRAFT. The final version is available for preview.

TrainingMaterial 1.0 Request for Comments

Published: 25 March 2022
Tags: Profile TrainingMaterial RequestForComment

The Training Working Group have requested that the community consider the TrainingMaterial profile for release based on the current 0.9-DRAFT. The final version is available for preview.

FAIR-Checker released

Published: 23 March 2022
Tags: Validation Software

We are pleased to announce the latest release of FAIR-Checker, a FAIR automated assessment tool, available at https://fair-checker.france-bioinformatique.fr

Three Deployments of the TrainingMaterial Profile

Published: 22 March 2022
Tags: Deployment TrainingMaterial

The Training Working Group are finalising the TrainingMaterial Profile and have added three live deployments of the profile. The first is for a lecture series on Biomedical semantics, information retrieval and knowledge discovery. The second is for a collection of tutorials on eNanoMapper. The third is for the training materials associated with a workshop on NanoSafety and the Semantic Web.

RiskGONE annotates nanomaterials with ChemicalSubstance

Published: 08 March 2022
Tags: ChemicalSubstance Deployment

The H2020 project RiskGONE started annotating nanomaterials they study in their research into risk governance with ChemicalSubstance (0.4-RELEASE) and European Registry of Materials identifiers.

Deployment of Protein Profile by PSnpBind

Published: 08 March 2022
Tags: Deployment Protein

Visualizing computing results for manual inspection is important. Ammar Ammar published (doi:10.1186/s13321-021-00573-5) 0.6 million ligand-protein docking experiments for 26 different protein structures with many single nucleotide polymorphisms in the online and open source PSnpBind database. The protein summary pages are annotated with the Protein profile (0.11-RELEASE) , for example for this Urokinase-type plasminogen activator.

Dataset Profile 0.5-DRAFT Published

Published: 28 February 2022
Tags: Profile Dataset

We are pleased to announce the latest draft release of the Dataset Profile from the Datasets Working Group. This iteration, together with the 0.4-DRAFT refreshes the profile bringing in the latest changes to the Schema.org Dataset properties and fixes a few issues that had been identified whilst deploying the profile (see the summary of changes on the 0.4 and 0.5 drafts).

Deployment of ComputationalTool Profile by PathVisio

Published: 26 January 2022
Tags: Deployment ComputationalTool

PathVisio is a tool for analysing and editing biological pathways used by WikiPathways. They have added ComputationalTool markup within their web page.

Deployment of BioSample Profile by EBISC

Published: 16 December 2021
Tags: Deployment BioSample

Building on the earlier work to add markup into The Human Pluripotent Stem Cell Registry (hPSCreg), the team have now deployed BioSample markup in the European Bank for Induced pluripotent Stem Cells (EBiSC registry).

Tutorial at SWAT4HCLS 2022

Published: 13 December 2021
Tags: Tutorial

At SWAT4HCLS 2022 we will be giving a tutorial on deploying and harvesting Bioschemas markup.

Deployment by RDMkit

Published: 29 November 2021
Tags: Deployment Person

The ELIXIR Research Data Management Kit (RDMkit) is an online guide containing good data management practices applicable to research projects from the beginning to the end. Developed and managed by people who work every day with life science data, the RDMkit has guidelines, information, and pointers to help you with problems throughout the data’s life cycle.

Deployment by MetaNetX

Published: 11 November 2021
Tags: Deployment MolecularEntity

MetaNetX, a database of automated model construction and genome annotation for large-scale metabolic networks, has deployed the MolecularEntity profile on over 1 million pages. The pages have been indexed in a sitemap to enable the harvesting of data.

Deployment by Protein Ensemble

Published: 08 November 2021
Tags: Deployment DataCatalog Dataset Organization Protein SequenceAnnotation SequenceRange ScholarlyArticle

Protein Ensemble (PED), is a deposition database of structural ensembles, with an emphasis on those known to be intrinsically disordered. While the PED deployment has been in place for about a year, it was not added to our live deploy list. PED have recently updated their deployment to include links to scholarly articles.

Deployment by Bgee

Published: 08 November 2021
Tags: Deployment Gene

Bgee, the gene expression data in animals database, has deployed the Gene profile on over 750,000 pages across 30 species. This will soon go up to 52 species with an increase in the number of pages containing markup. The pages have been indexed in a sitemap to enable the harvesting of data.

ComputationalTool Profile 1.0-RELEASE Published

Published: 02 November 2021
Tags: Profile ComputationalTool

We are pleased to announce the release of the ComputationalTool Profile from the Tools Working Group.

Standard Properties

Published: 01 November 2021
Tags: Community Profile

A standard set of properties have been added to all Bioschemas profiles. These properties allow consumers of markup to more easily understand the markup, and to validate it against the relevant profile. Essentially the properties form a boilerplate for any markup, see following code snippet for an example protein taken from DisProt.

Revised Sequences Profiles Published

Published: 11 October 2021
Tags: Profile Gene Protein SequenceAnnotation SequenceRange

The following profiles have been updated to allow the linking of sequence annotations to genes and proteins:

Gene 1.0-RELEASE –> Gene 1.1-DRAFT – adds a property to connect a gene to a SequenceAnnotation
Protein 0.11-RELEASE –> Protein 0.12-DRAFT – adds a property to connect a protein to a SequenceAnnotation
ProteinAnnotation 0.6-DRAFT –> SequenceAnnotation 0.7-DRAFT – note that this deprecates the ProteinAnnotation profile; generalising it to SequenceAnnotation
Adds the SequenceRange 0.1-DRAFT profile

ComputationalTool 1.0 Request for Comments

Published: 11 October 2021
Tags: Profile ComputationalTool RequestForComment

The Tools Working Group have requested that the community consider their current draft of the ComputationalTool Profile 0.6-DRAFT to become 1.0-RELEASE. There are two minor changes between the draft and release version:

Website Rebuild

Published: 22 September 2021
Tags: Community

Today we have deployed a major rewrite of our website which has been overseen by Bert Droesbeke.

Towards better findability: Bioschemas meets Schema.org

Published: 07 July 2021
Tags: Schema.org Type

On 7 July 2021, Schema.org included five Bioschemas types for representing life sciences data in its latest release. This update signifies an important step towards developing web markup in the life sciences. It will improve the findability of many web resources in the domain and ultimately translate into more efficient research.

Deployment of BioSample Profile by hPSCreg

Published: 30 June 2021
Tags: Deployment BioSample

The Human Pluripotent Stem Cell Registry (hPSCreg) have made the first deployment of the BioSample profile.

Deployments by the Plant Community

Published: 04 June 2021
Tags: Deployment Gene Study Taxon

The Plant Community have added two sites to our live deployment list.

CorkOakDB have deployments of the Gene and Taxon profiles.
PIPPA: PSB Interface for Plant Phenotype Analysis have deployments of the Study and Taxon profiles.