pan-metazoan anatomy knowledge base
terrestrial, marine
Joined January 2013
- Tweets154
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uberanat retweeted
Our short paper "Creation and unification of development and life stage ontologies for animals" (@ANiknejad @chrismungall Osumi-Sutherland @marc_rr @fred_bstn) is in the #ismb2022 @bioontologies Zenodo collection zenodo.org/record/6945852
All the collection zenodo.org/communities/bio-o…
uberanat retweeted
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.
uberanat retweeted
There are many other examples - you can see in @FAIRsharing_org some of these dependencies, for example Uberon below (and this misses many dependencies e.g @Hubmap @LINCSProgram ...)
ALT Graph of standards that use Uberon from FAIRsharing
uberanat 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
uberanat retweeted
Our preprint on ODK, the #OntologyDevelopmentKit is up on @arxiv arxiv.org/abs/2207.02056. Thanks to @shawnzktan @NicoMatentzoglu 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/
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uberanat retweeted
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/UBER… @uberanat #PenisOntology
Thanks for the shout-out, much appreciated! Fantastic work!
9/ This study stands on some terrific early work by then undergrad Marc Maldaver, along w/ contrib. from @annakopoulos & Lindsay Guare.
Also thanks to folks at Uberon & Cell Ontology for maintaining these resources! Kudos to @ArrayExpressEBI for great work w/ curating #metadata.
uberanat retweeted
1/ How can we all find & use >1mi public human omics samples when most #metadata is unstructured text?
In our new preprint, @nat_hawkins_ proposes a new method to classify unstruct. sample metadata to terms in a tissue ontology by combining #NLP & #ML.
doi.org/10.1101/2021.05.10.4…
uberanat retweeted
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
uberanat retweeted
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/
uberanat retweeted
Hacker News has @OBOFoundry on the front page! Lots of good comments, some critical (and fair). Hope to get round thi addressing these.
The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data mdpi.com/1424-2818/11/10/202
Visualizing comparisons between Uberon and species-specific ontologies and brain atlases with obographviz
New release of obographviz on npm - now with visualization of equivalence cliques; can be used to visualize similarity in two ontologies, e.g. human and mouse phenotype ontologies, or @uberanat and allen brain atlases. See wordpress.com/post/douroucou…
uberanat retweeted
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#/res…
genes from uniprot.org/uniprot/?query=r… #biocuration2019
uberanat retweeted
#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/20… (1/6)
uberanat retweeted
My paper is finally out that makes me very happy :) It provides the solutions to the tail-color problem and discusses many issues of trait coding and modeling.
Integration of anatomy ontologies and evo-devo using structured Markov models ... academic.oup.com/sysbio/adva…
uberanat retweeted
Nice to see that @uberanat is making an appearance at TDWG
Lise Stork now talking ontology, work flow and annotiations to get information out of the handwritten field books. #spnhctdwgNZ
