ontogpt_dissco_machine_annotation_service
https://github.com/senckenberg-dcbiodivit/ontogpt_dissco_machine_annotation_service
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.1%) to scientific vocabulary
Last synced: 9 months ago
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JSON representation
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Repository
Basic Info
- Host: GitHub
- Owner: Senckenberg-DCBiodivIT
- License: mit
- Language: Python
- Default Branch: main
- Size: 5.52 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Created about 1 year ago
· Last pushed about 1 year ago
Metadata Files
Readme
License
Citation
README.md
ontogptdisscomachineannotationservice
Installation
bash
pip install -r requirements.txt
Run
bash
python service.py
or
bash
fastapi run service.py
Configuration
The app can be configured via pydantic-settings. See here
| Setting | Description | Default | | ------- | ----------- | ------- | | loglevel | log level | INFO | | templatepath | Path to otogpt template | habitattemplatev2.yaml | | llm_model | LLM model to use | ollama/mistral |
TODO: Document/Configure how to use bioportal api key
Develop
For develop, you can run it in dev mode which automatically reload changes
bash
fastapi dev service.py
Owner
- Name: Senckenberg Digital Collection and Biodiversity Information Technologies @ Senckenberg
- Login: Senckenberg-DCBiodivIT
- Kind: organization
- Location: Germany
- Repositories: 1
- Profile: https://github.com/Senckenberg-DCBiodivIT
FAIR data specialists and research software engineers working towards interlinking, harmonization and facilitation of access to geobiodiversity research data.
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use OntoGPT, please cite it as follows."
authors:
- family-names: "Caufield"
given-names: "J. Harry"
orcid: "https://orcid.org/0000-0001-5705-7831"
- family-names: "Hegde"
given-names: "Harshad"
orcid: "https://orcid.org/0000-0002-2411-565X"
- family-names: "Emonet"
given-names: "Vincent"
orcid: "https://orcid.org/0000-0002-1501-1082"
- family-names: "Harris"
given-names: "Nomi L."
orcid: "https://orcid.org/0000-0001-6315-3707"
- family-names: "Joachimiak"
given-names: "Marcin P."
orcid: "https://orcid.org/0000-0001-8175-045X"
- family-names: "Matentzoglu"
given-names: "Nicolas"
orcid: "https://orcid.org/0000-0002-7356-1779"
- family-names: "Kim"
given-names: "HyeongSik"
orcid: "https://orcid.org/0000-0002-3002-9838"
- family-names: "Moxon"
given-names: "Sierra A.T."
orcid: "https://orcid.org/0000-0002-8719-7760"
- family-names: "Reese"
given-names: "Justin T."
orcid: "https://orcid.org/0000-0002-2170-2250"
- family-names: "Haendel"
given-names: "Melissa A."
orcid: "https://orcid.org/0000-0001-9114-8737"
- family-names: "Robinson"
given-names: "Peter N."
orcid: "https://orcid.org/0000-0002-0736-9199"
- family-names: "Mungall"
given-names: "Christopher J."
orcid: "https://orcid.org/0000-0002-6601-2165"
title: "OntoGPT"
version: 0.3.8
date-released: 2024-02-08
url: "https://github.com/monarch-initiative/ontogpt"
doi: 10.5281/zenodo.7894107
preferred-citation:
type: article
authors:
- family-names: "Caufield"
given-names: "J. Harry"
orcid: "https://orcid.org/0000-0001-5705-7831"
- family-names: "Hegde"
given-names: "Harshad"
orcid: "https://orcid.org/0000-0002-2411-565X"
- family-names: "Emonet"
given-names: "Vincent"
orcid: "https://orcid.org/0000-0002-1501-1082"
- family-names: "Harris"
given-names: "Nomi L."
orcid: "https://orcid.org/0000-0001-6315-3707"
- family-names: "Joachimiak"
given-names: "Marcin P."
orcid: "https://orcid.org/0000-0001-8175-045X"
- family-names: "Matentzoglu"
given-names: "Nicolas"
orcid: "https://orcid.org/0000-0002-7356-1779"
- family-names: "Kim"
given-names: "HyeongSik"
orcid: "https://orcid.org/0000-0002-3002-9838"
- family-names: "Moxon"
given-names: "Sierra A.T."
orcid: "https://orcid.org/0000-0002-8719-7760"
- family-names: "Reese"
given-names: "Justin T."
orcid: "https://orcid.org/0000-0002-2170-2250"
- family-names: "Haendel"
given-names: "Melissa A."
orcid: "https://orcid.org/0000-0001-9114-8737"
- family-names: "Robinson"
given-names: "Peter N."
orcid: "https://orcid.org/0000-0002-0736-9199"
- family-names: "Mungall"
given-names: "Christopher J."
orcid: "https://orcid.org/0000-0002-6601-2165"
doi: "10.1093/bioinformatics/btae104"
journal: "Bioinformatics"
title: "Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning"
year: 2024
url: https://doi.org/10.1093/bioinformatics/btae104
GitHub Events
Total
- Member event: 1
- Push event: 17
- Create event: 2
Last Year
- Member event: 1
- Push event: 17
- Create event: 2
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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Dependencies
requirements_inference.txt
pypi
- ontogpt ==1.0.10
- requests ==2.32.3
requirements_service.txt
pypi
- fastapi ==0.112.2
- uvicorn ==0.30.6
- websocket-client ==1.8.0
- websockets ==13.1