pan-metazoan anatomy knowledge base
Joined January 2013
- Tweets 154
- Following 140
- Followers 136
- Likes 10
4 Photos and videos
uberanat retweeted
8 Aug 2022
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…
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uberanat retweeted
15 Jul 2022
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.
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uberanat retweeted
15 Jul 2022
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
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uberanat retweeted
15 Jul 2022
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
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uberanat retweeted
6 Jul 2022
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
28 Aug 2021
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
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Thanks for the shout-out, much appreciated! Fantastic work!
13 May 2021
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.
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uberanat retweeted
14 May 2021
13 May 2021
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…
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uberanat retweeted
Lady Gaga as sea urchins - a thread
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uberanat retweeted
6 Oct 2020
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
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uberanat retweeted
14 Feb 2020
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/
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uberanat retweeted
22 Jan 2020
Hacker News has @OBOFoundry on the front page! Lots of good comments, some critical (and fair). Hope to get round thi addressing these.
21 Jan 2020
OboFoundry on the front page of HN :) news.ycombinator.com/item?id…
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The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data mdpi.com/1424-2818/11/10/202
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Visualizing comparisons between Uberon and species-specific ontologies and brain atlases with obographviz
10 May 2019
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…
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uberanat retweeted
9 Apr 2019
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
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uberanat retweeted
9 Mar 2019
#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)
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uberanat retweeted
22 Jan 2019
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…
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uberanat retweeted
27 Aug 2018
Nice to see that @uberanat is making an appearance at TDWG
27 Aug 2018
Lise Stork now talking ontology, work flow and annotiations to get information out of the handwritten field books. #spnhctdwgNZ
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