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Create CITATION.cff
References https://zenodo.org/records/13151195 Co-authored-by: Elizabeth Campolongo <[email protected]>
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‎.zenodo.json‎

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{
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"creators": [
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{
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"name": "Bradley, John",
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"orcid": "0000-0003-3858-848X"
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},
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{
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"name": "Lapp, Hilmar",
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"orcid": "0000-0001-9107-0714"
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},
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{
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"name": "Campolongo, Elizabeth G.",
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"orcid": "0000-0003-0846-2413"
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}
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],
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"description": "Python package and command line tool that simplifies using the BioCLIP foundation model.",
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"keywords": [
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"clip",
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"biology",
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"CV",
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"imageomics",
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"animals",
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"species",
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"images",
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"taxonomy",
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"rare species",
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"endangered species",
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"evolutionary biology",
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"multimodal",
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"knowledge-guided",
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"python",
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"command line",
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"bioclip",
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"plants",
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"fungi",
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"genus",
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"image classification"
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],
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"license": {
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"id": "MIT"
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},
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"publication_date": "2024-07-19",
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"title": "pybioclip",
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"version": "1.0.0",
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"funding": [
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{
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"award": {
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"id": "021nxhr62::2118240",
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"number": "2118240",
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"program": "CISE/OAD",
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"title": {
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"en": "HDR Institute: Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning"
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}
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},
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"funder": {
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"id": "021nxhr62",
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"name": "National Science Foundation"
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}
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}
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],
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"references": [
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{
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"reference": "Stevens S, Wu J, Thompson MJ, Campolongo EG, Song CH, Carlyn DE, Dong L, Dahdul WM, Stewart C, Berger-Wolf T, Chao W-L, Su Y (2024) BioCLIP: A Vision Foundation Model for the Tree of Life. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 19412\u201319424."
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},
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],
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"related_identifiers": [
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{
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"identifier": "https://github.com/Imageomics/pybioclip/",
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"relation_type": {
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"id": "isversionof",
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"title": {
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"de": "Ist eine Version von",
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"en": "Is version of"
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}
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},
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"resource_type": {
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"id": "software",
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"title": {
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"de": "Software",
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"en": "Software"
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}
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},
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"scheme": "url"
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}
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],
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"resource_type": {
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"id": "software",
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"title": {
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"de": "Software",
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"en": "Software"
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}
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}
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}

‎CITATION.cff‎

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cff-version: 1.2.0
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title: pybioclip
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message: If you use this software, please cite both the conference paper from references section and the software itself.
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type: software
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authors:
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- given-names: John
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family-names: Bradley
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- given-names: Hilmar
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family-names: Lapp
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- family-names: Campolongo
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given-names: "Elizabeth G."
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identifiers:
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- type: doi
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value: 10.5281/zenodo.13151194
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- description: "The GitHub release URL of tag 1.0.0."
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type: url
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value: "https://github.com/Imageomics/pybioclip/releases/tag/1.0.0"
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- description: "The GitHub URL of the commit tagged with 1.0.0."
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type: url
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value: "https://github.com/Imageomics/pybioclip/tree/19b3c52a9b806a4abfd1c847ba2ebb6a4d703b34"
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repository-code: 'https://github.com/Imageomics/pybioclip'
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url: 'https://github.com/Imageomics/pybioclip'
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abstract: Python package and command line tool that simplifies using the BioCLIP foundation model.
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keywords:
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- clip
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- biology
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- CV
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- imageomics
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- animals
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- species
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- images
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- taxonomy
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- "rare species"
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- "endangered species"
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- "evolutionary biology"
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- multimodal
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- "knowledge-guided"
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- python
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- "command line"
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- bioclip
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- plants
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- fungi
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- genus
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- "image classification"
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license: MIT
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version: 1.0.0
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date-released: '2024-07-19'
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preferred-citation:
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authors:
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- given-names: John
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family-names: Bradley
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- given-names: Hilmar
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family-names: Lapp
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- family-names: Campolongo
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given-names: "Elizabeth G."
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type: software
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title: pybioclip
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version: 1.0.0
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doi: 10.5281/zenodo.13151194
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date-released: "2024-07-19"
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references:
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- type: conference-paper
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title: "BioCLIP: A Vision Foundation Model for the Tree of Life"
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authors:
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- family-names: Stevens
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given-names: Samuel
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- family-names: Wu
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given-names: Jiaman
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- family-names: Thompson
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given-names: "Matthew J."
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- family-names: Campolongo
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given-names: "Elizabeth G."
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- family-names: Song
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given-names: "Chan Hee"
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- family-names: Carlyn
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given-names: "David Edward"
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- family-names: Dong
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given-names: Li
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- family-names: Dahdul
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given-names: "Wasila M"
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- family-names: Stewart
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given-names: Charles
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- family-names: "Berger-Wolf"
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given-names: Tanya
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- family-names: Chao
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given-names: "Wei-Lun"
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- family-names: Su
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given-names: Yu
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version: 1.0.0
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doi: "10.5281/zenodo.10895871"
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date-released: "2024-03-29"

‎README.md‎

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## Acknowledgments
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The [prediction code in this repo](src/bioclip/predict.py) is based on work by [@samuelstevens](https://github.com/samuelstevens) in [bioclip-demo](https://huggingface.co/spaces/imageomics/bioclip-demo/tree/ef075807a55687b320427196ac1662b9383f988f).
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## Citation
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Our code (this repository):
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```
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@software{Bradley_pybioclip_2024,
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author = {Bradley, John and Lapp, Hilmar and Campolongo, Elizabeth G.},
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doi = {10.5281/zenodo.13151194},
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month = jul,
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title = {{pybioclip}},
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version = {1.0.0},
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year = {2024}
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}
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```
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BioCLIP paper:
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```
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@inproceedings{stevens2024bioclip,
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title = {{B}io{CLIP}: A Vision Foundation Model for the Tree of Life},
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author = {Samuel Stevens and Jiaman Wu and Matthew J Thompson and Elizabeth G Campolongo and Chan Hee Song and David Edward Carlyn and Li Dong and Wasila M Dahdul and Charles Stewart and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
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booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
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year = {2024}
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}
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```
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Also consider citing the BioCLIP code:
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```
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@software{bioclip2023code,
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author = {Samuel Stevens and Jiaman Wu and Matthew J. Thompson and Elizabeth G. Campolongo and Chan Hee Song and David Edward Carlyn},
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doi = {10.5281/zenodo.10895871},
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title = {BioCLIP},
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version = {v1.0.0},
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year = {2024}
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}
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```

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