typedb-bio
scispacy
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| typedb-bio | scispacy | |
|---|---|---|
| 1 | 2 | |
| 73 | 1,615 | |
| - | 2.7% | |
| 4.6 | 6.7 | |
| 10 months ago | about 1 month ago | |
| Python | Python | |
| - | Apache License 2.0 |
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Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
typedb-bio
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How Roche Discovered Novel Potential Gene Targets with TypeDB
For this purpose, David built out a set of rules and schema in TypeQL. Below is just a very small excerpt of how such data can be modelled — taken from BioGrakn-Covid, a Vaticle community-led project by Konrad Mysliwiec (Data Science Software Engineer, Roche). Note that this is a selected schema; the full schema can be found within the BioGrakn-Covid schema file.
scispacy
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Guidance needed: Extracting diseases and symptoms from medical text
https://github.com/medspacy/medspacy and https://allenai.github.io/scispacy/ should get you most of the way there
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Installing SciSpacy on Apple M1 Laptops
The ** pip install -r requirement.txt ** failed with lot of errors while installing a dependency ** nmslib ** with an error ** clang compiler does not support '-march=native' **. Since I already had the Xcode installed on my Mac the version of C was 11 but somehow the mentioned command was failing, since the said argument was not supported on the C version. With a lot of digging around I finally found a solution mentioned on SciSpacy GitHub page.
What are some alternatives?
grakn - TypeDB: the polymorphic database powered by types
medspacy - Library for clinical NLP with spaCy.
obsidian-garden - A knowledge management garden for https://obsidian.md, in which to grow your ideas
rasa - 💬 Open source machine learning framework to automate text- and voice-based conversations: NLU, dialogue management, connect to Slack, Facebook, and more - Create chatbots and voice assistants
topic-db - TopicDB is a topic maps-based semantic graph store (using SQLite for persistence)
spaCy - 💫 Industrial-strength Natural Language Processing (NLP) in Python
pygraft - Configurable Generation of Synthetic Schemas and Knowledge Graphs at Your Fingertips
spacy-models - 💫 Models for the spaCy Natural Language Processing (NLP) library
codex - CoDEx: A set of knowledge graph Completion Datasets Extracted from Wikidata and Wikipedia
SigProfilerExtractor - SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
ckb - Contextual knowledge bases