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Input
string | Base64
string | txt
string | Output
string | PDF_Name
string |
|---|---|---|---|---|
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AEYAcgBvAHoAZQBuACAAVABpAHMAcwB1AGUAIABOAHUAYwBsAGUAaQAgAEU(...TRUNCATED) | "ABSTRACT\nFrozen Tissue Nuclei Extraction (v2)\nCarly Martin\n, \nAbdul Abdul\n, \nCharles Vanderbu(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nExtraction of nuclei from frozen tissue for single-nuclei sequenci(...TRUNCATED) | frozen-tissue-nuclei-extraction-v2-7xchpiw.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AFAAcgBvAHQAbwBjAG8AbAAgAGYAbwByACAAYQAgAG4AYQB0AGkAbwBuAHc(...TRUNCATED) | "Aug 12, 2022\nProtocol for a nationwide systematic\nreview of the Greek literature on child and\nad(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nThe goal of this experiment is to conduct a nationwide systematic (...TRUNCATED) | protocol-for-a-nationwide-systematic-review-of-the-ce8fthtn.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/ADIAJQAgAEEAZwBhAHIAbwBzAGUAIABHAGUAbCkKL0NyZWF0b3IgKP7/AHc(...TRUNCATED) | "Jun 03, 2022\n2% Agarose Gel\nGeorge \nTesto\nThe Pathogen & Microbiome Institute\n \nprotocol\n \n(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nTo prepare and use a 2% agarose gel for the separation and analysi(...TRUNCATED) | 2-agarose-gel-cac7sazn.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKJeLjz9MKJVBERi0xLjQKJeLjz9MKMyAwIG9iago8PC9UeXBlIC9QYWdlCi9QYXJlbnQgMSAwIFIKL01lZGlhQm9(...TRUNCATED) | "1 Published: 10 Jan 2018\nThis is an open access protocol distributed under the terms of the Creat(...TRUNCATED) | "```markdown\nGoal/Experiment:\n\nThe goal of this experiment is to assess coastal flood risk and th(...TRUNCATED) | assessing-coastal-risk-and-the-economics-of-climat-miyc4fw.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKJeLjz9MKJVBERi0xLjQKJeLjz9MKMyAwIG9iago8PC9UeXBlIC9QYWdlCi9QYXJlbnQgMSAwIFIKL01lZGlhQm9(...TRUNCATED) | "1 Published: 04 Sep 2017\nThis is an open access protocol distributed under the terms of the Creat(...TRUNCATED) | "```markdown\n# High quality DNA extraction protocol from recalcitrant plant tissues\n\n## Goal/Expe(...TRUNCATED) | high-quality-dna-extraction-protocol-from-recalcit-i8jchun.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AEcAZQBuAGUAcgBhAGwAIABnAGUAbgBvAHQAeQBwAGkAbgBnACAAbwBmAKA(...TRUNCATED) | "NOV 10, 2023\nGeneral genotyping of Myzus persicae using PCR with\nmicrosatellite markers and gel e(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nGeneral Genotyping of Myzus persicae using PCR with Microsatellite(...TRUNCATED) | general-genotyping-of-myzus-persicae-using-pcr-wit-c4tnywme.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AEYAaQB4AGEAdABpAG8AbgAgAGEAbgBkACAAcwB0AGEAaQBuAGkAbgBnACA(...TRUNCATED) | "FEB 07, 2023\nFixation and staining of gemmule-hatched Ephydatia\nmuelleri \nfor fluorescence micro(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nFixation and staining of gemmule-hatched Ephydatia muelleri for fl(...TRUNCATED) | fixation-and-staining-of-gemmule-hatched-ephydatia-cnzdvf26.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AEkAbQBhAGcAZQAgAHAAcgBvAGMAZQBzAHMAaQBuAGcAIAB0AG8AIABpAG4(...TRUNCATED) | "JUL 31, 2023\nImage processing to investigate NEMO recruitment\nand involvement in mitophagy and in(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nImage processing to investigate NEMO recruitment and involvement i(...TRUNCATED) | image-processing-to-investigate-nemo-recruitment-a-cbvjsn4n.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AFMAbQBhAGwAbAAgAHYAbwBsAHUAbQBlACAAZgB1AG4AZwBhAGwAIABnAGU(...TRUNCATED) | "Nov 03, 2021\nSmall volume fungal genomic DNA\nextraction protocol for \nIllumina genome\n \nV.1\nJ(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nHigh molecular weight DNA extraction from hyphae of filamentous fu(...TRUNCATED) | small-volume-fungal-genomic-dna-extraction-protoco-3w9gph6.pdf |
Convert the PDF file to markdown format | "JVBERi0xLjQKMSAwIG9iago8PAovVGl0bGUgKP7/AFAAcgBvAHQAbwBjAG8AbAAgAHQAbwAgAHAAcgBvAGMAZQBzAHMAIABHAGE(...TRUNCATED) | "Jun 02, 2021\nProtocol to process Gastruloids for FACS (reporters only) \nStefano \nVianello\n,\nTa(...TRUNCATED) | "```markdown\n# Goal/Experiment:\nProtocol to process reporter Gastruloids for FACS analysis of thei(...TRUNCATED) | protocol-to-process-gastruloids-for-facs-reporters-bvgrn3v6.pdf |
End of preview.
Caduceus Project Dataset
Creator: Kquant03
About the Dataset: The Caduceus Project Dataset is a curated collection of scientific and medical protocols sourced from protocols.io and converted from PDF to markdown format. This dataset aims to help models learn to read complicated PDFs by either using computer vision on the PDF file, or through processing the raw text directly. You can find the repository for the pipeline here.
Source Data:
- Protocols from protocols.io
Key Features:
- Carefully selected high-quality protocols
- Base64 encodings for potential vision training
- Guaranteed quality through hand processing the resulting data
Dataset Structure:
pdf_files/: Contains the original PDF files of the selected protocols.markdown_files/: Contains the individual markdown files converted from the selected PDF files.Caduceus_Data.jsonl/: A JSONL file including an input field, a Base64 encoding of the PDF file, the raw text from the PDF, the formatted markdown output, and the name of the corresponding file.
License: The Caduceus Project Dataset is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License.
Acknowledgments: We would like to express our gratitude to the contributors of protocols.io for providing the open-source repository of scientific and medical protocols that served as the foundation for this dataset.
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