The OntoWeaver team is proud to release version 1.4 of its tool 🥳

OntoWeaver allows to easily parse iterable data (like tables or documents) and create a Semantic Knowledge Graph. Basically, you write a simple YAML file telling what data you want to be a node or a property, you call a generic command, and 🎉 , you have your graph ready.

With the 1.4 series, the main new feature is an option to display progress bars when doing heavy processing (like loading large CSV files).

The documentation has also been heavily updated, completed and polished:
https://ontoweaver.readthedocs.io/en/latest

#python #SKG #KG #graph #neo4j #ontoweaver #biocypher #science #bioinformatics #pasteur #ontologies #semanticWeb

The OntoWeaver team is proud to release version 1.3 of its tool 🥳

OntoWeaver allows to easily parse iterable data (like tables or documents) and create a Semantic Knowledge Graph. Basically, you write a simple YAML file telling what data you want to be a node or a property, you call a generic command, and 🎉 , you have your graph ready.

We've been using OntoWeaver on a few real use-cases, I think it's now in a pretty good state, and ready for you to use. We recently put a lot of attention on the documentation, with tutorials and a primer about KG for newcomers: https://ontoweaver.readthedocs.io/en/latest

With the 1.3 series, the main new features are:
* `ontoweave` can now load multiple compatible data files at once, for the same mapping, with a classical "shell glob". E.G. `ontoweave data/*.parquet:mapping.yaml`
* OntoWeaver now has the ability to automatically create or extend a BioCypher schema from the mapping (useful if you don't want to type a large but straightforward set of types!).

Get the code at: https://github.com/oncodash/ontoweaver or using `pip`: https://pypi.org/project/ontoweaver/

#python #SKG #graph #ontoweaver #biocypher #science #bioinformatics #pasteur #ontologies #semanticWeb

We are happy to announce the release of the 1.2 version of OntoWeaver, the tool that sits on top of BioCypher and allows to easily make independent adapters parsing structure data, from just a simple declaration of a mapping: https://github.com/oncodash/ontoweaver/releases/tag/v1.2.0

The main new feature is adapters for structured documents: OWL (ontology files' populated graph), XML and JSON documents, and some new high-level information fusion functions.

The package is available on PyPI, now in the BioCypher community: https://pypi.org/project/ontoweaver/1.2.0/

#ontoweaver #biocypher #knowledgeGraphs #ontologies #semantic #biomedicine #science #freesoftware #python

Very proud to say that our two Master interns of this year did an awesome job. To the point that they won the "André Blanc-Lapierre Île-de-France" prize, from the SEE (one of the oldest academic societies in France). This is well-deserved 🏆

https://www.linkedin.com/posts/asso-see_prixjeunes-grandsprixsee2024-prixblanclapierre-activity-7271928658376757248-25L1

They even participated to scientific publications 📝
For more information, see:
- 🦀 "High-level Biomedical Data Integration in a Semantic Knowledge Graph with OncodashKB for finding Personalized Actionable Drugs in Ovarian Cancer" — https://lnkd.in/eqiSNF7g and
- 🧮 "Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher" — https://lnkd.in/evPU_th5

@OpenSci_Pasteur
#science #KnowledgeGraph #semantics #OntoWeaver #OncodashKB #Oncodash #OpenScience

#HelloESR I'm a Senior/Expert Research Engineer in #Bioinformatics. I've been working as a researcher in hybrid #AI #Algorithmics (i.e. #metaheuristic optimization) for 20 years, but I'm now interested in engineering Semantic Knowledge Graphs stuff into Decision Support Systems & #ExplainableAI #XAI.

I compute Biomedicine against #Cancer at Institut Pasteur.

I'm the #ParadisEO (an optim framework), #Oncodash (tumor board #DSS), and #OntoWeaver (easy creation of #SKG on top of #BioCypher) maintainer.