A simple but expressive YAML-based data modeling language for effortlessly adding semantics to your data. https://xitter.cf/t.co/vNvm6hotvh
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Joined July 2021
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LinkML - Linked (Open) Data Modeling Language retweeted
The video of Sierra Moxon's ISCBacademy webinar (LinkML: an open data modeling framework, grounded with ontologies) is now up at youtube.com/watch?v=nyNp09WY… and the slides are at docs.google.com/presentation…
LinkML - Linked (Open) Data Modeling Language retweeted
🙌Closer to bridging the gap between #biodiversity #omics data standards!
🆕Methods paper - part of the @Bicikl_H2020 collection - reports on building sustainable #interoperability between @tdwg's Darwin Core and MIxS.
Find more: blog.pensoft.net/2023/10/04/…
#GEOBONconf2023 #TDWG2023
LinkML - Linked (Open) Data Modeling Language retweeted
Take xitter.cf/semanticbeeng/status/1… (thread)
I think it is necessary to have #typelevel (schema) #datalineage across tech, languages, ML workflows ("data pipelines") + bring closer #dataengineering and #datagovernance in order to realize #ResponsibleAI
And #LinkML is uniquely suited
A #SemanticLayer needs a data schema language that can
1. subsume existing schema languages: json, avro, etc
2. abstract over data formats (delay conversions)
3. use a generative approach towards existing schema dialects, #GPL-s & frameworks
linkml.io/linkml/faq/why-lin…
#SmartData
LinkML - Linked (Open) Data Modeling Language retweeted
LinkML github.com/linkml is a great eco-system. Did some experimenting with multiple data model paradigms and dito data serialisations with the same semantics. LinkML is built with itself! @oeg_upm @semanticbeeng @mijaspao @kvistgaard @linkml_data What do you think?
LinkML - Linked (Open) Data Modeling Language retweeted
A #SemanticLayer needs a data schema language that can
1. subsume existing schema languages: json, avro, etc
2. abstract over data formats (delay conversions)
3. use a generative approach towards existing schema dialects, #GPL-s & frameworks
linkml.io/linkml/faq/why-lin…
#SmartData
LinkML - Linked (Open) Data Modeling Language retweeted
"Data is self-describing and does not rely on an application for interpretation and meaning."
With @linkml_data we can have data stay in efficient data formats and "eat the semantic cake too" (on demand; keen conversion to RDF makes silos)
xitter.cf/semanticbeeng/status/1…
#SmartData
A #SemanticLayer needs a data schema language that can
1. subsume existing schema languages: json, avro, etc
2. abstract over data formats (delay conversions)
3. use a generative approach towards existing schema dialects, #GPL-s & frameworks
linkml.io/linkml/faq/why-lin…
#SmartData
LinkML - Linked (Open) Data Modeling Language retweeted
We added a howto guide to the @linkml_data docs on generating AI prompts from LinkML schemas. linkml.io/linkml/howtos/gene…, making use of the new feature in the @OpenAI API to structure results as JSON platform.openai.com/docs/gui… 🧵
LinkML - Linked (Open) Data Modeling Language retweeted
github.com/monarch-initiativ… will be of interest to folks using RDF who aren’t allergic to LLMs
The OntoGPT framework and SPIRES tool by @chrismungall 's team provide a principled approach to extract knowledge graph from unstructured text using GPT. Here is my impression. apex974.com/articles/ontogpt…
LinkML - Linked (Open) Data Modeling Language retweeted
#LinkML and #SodaCL could be combined to specify #DataContract-s with a semantic layer, in a technology agnostic way 🤔
linkml.io/linkml/intro/overv……
docs.soda.io/soda-cl/metrics…… cc
cc @linkml_data @Onehousehq @datahubproject
#SmartData
LinkML - Linked (Open) Data Modeling Language retweeted
The @MonarchInit Biolink Model Brings Data Together! Find out more about our top 3 most downloaded papers in 2022 from the journal ASCPT here: ascpt.org/Journals/CTS/Trans…
#BiolinkModel #TeamScience #Collaboration #RareDisease #DrugRepurposing #TranslationalScience @linkml_data
LinkML - Linked (Open) Data Modeling Language retweeted
Interesting use of GPT to build structured knowledge bases from unstructured text using Large Language Models. @chrismungall et al monarchinit.medium.com/spire…
LinkML - Linked (Open) Data Modeling Language retweeted
In Tuesday's @MonarchInit Semantic Engineering Training @N_Vasilevsky and I tried to hammer out one message: how attribution and appreciation fuel the Open Science movement.
LinkML - Linked (Open) Data Modeling Language retweeted
Looking forward to seeing all you ontology peeps at @ICBOconf and @us2ts next week. And I'm hoping many of you can make it to the @linkml_data tutorial and @OBOFoundry tools workshop icbo-conference.github.io/ic…
LinkML - Linked (Open) Data Modeling Language retweeted
In 2018, the model was formally defined using a YAML-based modeling language. The latter is now called LinkML. Take a look at @cmungall's thread (xitter.cf/chrismungall/status/15…) to learn about LinkML and its ecosystem.
New blog post on how @linkml_data helps use ontologies and vocabularies as part of data models and standards douroucouli.wordpress.com/20… 🧵
ALT Figure 2 from Ontology application and use at the ENCODE DCC (PMC4360730), showing how the ENCODE schema uses different ontologies like OBI, Uberon, and CHEBI in different contexts
LinkML - Linked (Open) Data Modeling Language retweeted
New blog post on how @linkml_data helps use ontologies and vocabularies as part of data models and standards douroucouli.wordpress.com/20… 🧵
ALT Figure 2 from Ontology application and use at the ENCODE DCC (PMC4360730), showing how the ENCODE schema uses different ontologies like OBI, Uberon, and CHEBI in different contexts
LinkML - Linked (Open) Data Modeling Language retweeted
I'm reaching the point where I come to the conclusion that doing RDF without data-contracts in SHACL shapes is a very slippery slope.
Pretty much anything can be represented in shapes and it reduces the error-surface tremendously because we can validate everything everywhere.
LinkML - Linked (Open) Data Modeling Language retweeted
Across OBO and LinkML land we tend to now simply use mkdocs for generating shiny documentation from markdown, and host it on GitHub pages, E.g linkml.io/linkml-model/docs/
LinkML - Linked (Open) Data Modeling Language retweeted
Sparlfun uses Jinja templates for flexible generative logic, and uses @linkml_data for well defined data models/shapes for your queries linkml.github.io/sparqlfun/h…
LinkML - Linked (Open) Data Modeling Language retweeted
Our preprint on Simple Standard for Sharing Ontology Mappings has been submitted and is up on @arxiv arxiv.org/abs/2112.07051. SSSOM is a datamodel and exchange format for mappings between database entities, #ontology terms, etc. Thanks to @NicoMatentzoglu for spearheading this!
LinkML - Linked (Open) Data Modeling Language retweeted
With over 13K terms, @hp_ontology can be leveraged as a powerful tool for differential #diagnostics, #PrecisionMedicine, and translational research.
We spoke with #HPO founder @drseb_ to understand how he expects this groundbreaking resource to develop.
bit.ly/3p67gO3