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#MakeUrOntologyAwesome: I'm starting a series of "top tips" for #ontology development, based on my experience working with bio-ontology editors on a variety of projects. douroucouli.wordpress.com/2019/03/09/ont… (1/6)

Had to try plugging a gene list from Genomics England into #TopAnat Bgee database: "Diabetes - neonatal onset” genes have strong expression enrichment in pancreas islet of Langerhans 👍 bgee.org/?page=top_anat… #biocuration2019 #shamelessselfpromotion

Also tried testing #TopAnat expression enrichment of genes coding for proteins annotated with Alzheimer’s in SwissProt UniProt: few genes so not very significant, but top frontal pole makes sense bgee.org/?page=top_anat… genes from uniprot.org/uniprot/?query… #biocuration2019

Visualizing comparisons between Uberon and species-specific ontologies and brain atlases with obographviz

I’ve hung around #ISMBECCB conferences long enough to see zoology becoming mainstream in #Bioinformatics #planaria #evodevo

The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data mdpi.com/1424-2818/11/1…

Hacker News has OBO Foundry on the front page! Lots of good comments, some critical (and fair). Hope to get round thi addressing these.

Happy #ValentinesDay! The 🤎 has been associated with love since ancient Greece. While humans only have one kind of 🤎, there is a large diversity of pumping organs in animals. Our #ComparativeAnatomy ontology Uberon (uberanat) has 12 different kinds of 🤎! Here are a few: 1/

There are many graph embedding algorithms, not all of them suitable for ontologies/KGs. Treating an ontology as a homogeneous graph omits information encoded in edge labels. Additionally, different edge labels have logical properties/rules (e.g. in uberon anatomy KG). 3/n

Lady Gaga as sea urchins - a thread

Hooray #uberon Monarch Initiative Chris Mungall #ontologies. Nice paper :-)

Thanks for the shout-out, much appreciated! Fantastic work!

Aella We have a wide range of intermittent organs in our animal anatomy ontology. They are all my faves. I see let's of great suggestions I this thread, we will have to add them! purl.obolibrary.org/obo/UBERON_000… uberanat #PenisOntology

Our preprint on ODK, the #OntologyDevelopmentKit is up on arXiv.org arxiv.org/abs/2207.02056. Thanks to @shawnzktan Nicolas Matentzoglu and the whole team for your work on this. This is a lot of work on infrastructure that makes things work behind the scenes. So what is ODK exactly? 1/

this delights me so. 🤣💛🔥

These specialised parasites (batflies) have co-evolved with their bat hosts for millions of years. They have developed a flat, hard body to prevent being crushed & velcro-like hairs & claws to hang on to their hosts' fur.

New blog post on how LinkML - Linked (Open) Data Modeling Language helps use ontologies and vocabularies as part of data models and standards douroucouli.wordpress.com/2022/07/15/usi… 🧵

There are many other examples - you can see in @fairsharing.bsky.social some of these dependencies, for example Uberon below (and this misses many dependencies e.g Hubmap LINCS Program ...)

Our short paper "Creation and unification of development and life stage ontologies for animals" (Anne Niknejad Chris Mungall Osumi-Sutherland Marc RobinsonRechavi @[email protected] Frederic Bastian) is in the #ismb2022 Bioontologies Zenodo collection zenodo.org/record/6945852 All the collection zenodo.org/communities/bi…

Welcome to twitter, cell_ontology!