We are pleased to announce that the Schema Playground publication from BMC Bioinformatics is available.
Published: 24 January 2023
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 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.
Published: 10 November 2022
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
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 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 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.
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.
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!
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.
We are pleased to announce the latest release of FAIR-Checker, a FAIR automated assessment tool, available at https://fair-checker.france-bioinformatique.fr
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.
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.
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).
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).
Published: 13 December 2021
At SWAT4HCLS 2022 we will be giving a tutorial on deploying and harvesting Bioschemas markup.
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.
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.
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.
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.
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.
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
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:
Published: 22 September 2021
Today we have deployed a major rewrite of our website which has been overseen by Bert Droesbeke.
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.
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.
The IMI Data Catalog, developed as part of the FAIRplus project, has been added to our live deployment list with deployments of the Dataset and DataCatalog profiles.
Published: 28 May 2021
Check out our revamped live deploy page.