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#researchtools

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Public
John Mackay

New tool for philosophers, scientists, & thinkers:
The Ontological Model Assessment Framework (OMAF) is now live on GitHub.
Evaluate _any_ ontology — in any domain — with clarity, structure, and rigor.

🔗 github.com/johnmackay61/omaf
#ontology #philosophy #researchtools #openscience

GitHubGitHub - johnmackay61/omaf: Ontological Model Assessment FrameworkOntological Model Assessment Framework. Contribute to johnmackay61/omaf development by creating an account on GitHub.
Public
Kohulan Rajan

New Preprint Alert!

We're excited to share our latest work on #ChemRxiv! MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures) is a web-based platform for extracting chemical information from scientific papers.

📄 Preprint: doi.org/10.26434/chemrxiv-2025

🔗 Try it out: marcus.decimer.ai

ChemRxivMARCUS: Molecular Annotation and Recognition for Curating Unravelled StructuresThe exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions operate in isolation, which limits their scalability for comprehensive literature curation. Here we present MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures), a tool to aid curators in performing literature curation in the field of natural products. This integrated web-based platform combines automated text annotation, multi-engine OCSR, and direct submission capabilities to the COCONUT database. MARCUS employs a fine-tuned GPT-4 model to extract chemical entities and utilises an ensemble approach integrating DECIMER, MolNexTR, and MolScribe for structure recognition. The platform aims to streamline the data extraction workflow from PDF upload to database submission, significantly reducing curation time. MARCUS bridges the gap between unstructured chemical literature and machine-actionable databases, enabling FAIR data principles and facilitating AI-driven chemical discovery. Through open-source code, accessible models, and comprehensive documentation, the web application enhances accessibility and promotes community-driven development. This approach facilitates unrestricted use and encourages the collaborative advancement of automated chemical literature curation tools. We dedicate MARCUS to Dr Marcus Ennis, the longest-serving curator of the ChEBI database, on the occasion of his 75th birthday.
#Cheminformatics#OpenScience#ChemicalDatabases
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Public
Ronja

(6/X) Migration update: Moving from Windows to Linux!
After 4 intense days, I’m pausing the move as I’ve run out of time. The biggest hurdle is migrating my research data. As a research librarian working on systematic reviews, I rely on reference managers and qualitative analysis tools, but I am struggling with compatibility issues — for example, EndNote/Atlasti (Windows) vs. Zotero/ Taguette (Linux).
#EndOf10 #Linux #Compatibility #ResearchTools #OpenSource #Technology #AskFedi @zotero

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Ronja

Switching from EndNote to Zotero? Not as smooth as I hoped.

Wanted:
export EndNote library with PDFs, notes & group structure
Got:
* no group export via RIS/XML, had to do it manually,
* double records for refs in multiple groups
* lost (research) notes
* syncing to Zotero web = painfully slow
* limited storage 2GB (have to pay 120$/year for unlimited storage)

#Zotero #EndNote #ResearchTools #ReferenceManager
#EndOf10 #Linux #LinuxMint #Compatibility #OpenSource #Technology #AskFedi

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Ronja

This is awful. I'm backing up my research data from EndNote + Atlas.ti because I can't use them on Linux. I tried switching to Zotero and Taguette, but the data migration process is problematic: I lost groups with Zotero and Taguette doesn't support QDPX file import. 😤
Does anyone know of a QDA tool for Linux that supports QDPX file import (Project Exchange Format for Qualitative Data)?
#EndOf10 #Linux #LinuxMint #ResearchTools #QDA #QDAsoftware #Compatibility #OpenSource #Technology #AskFedi

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Public
Ronja

@zotero Hello Zotero! I would love to migrate my EndNote library to Zotero. Is it possible to migrate not only the references within my groups, but also the entire group structure? I haven't been able to find a way to do this yet, so I would be very grateful if you could guide me through the process.

#Linux#ResearchTools#EndNote
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Ronja

(2/X) Migration update: Moving from Windows to Linux!
Most of my software have solid alternatives — switched from EndNote to Zotero for reference management.
But migrating everything (attachments, file structure/groups) from EndNote is proving tricky.
📚 If you know how to fully export an EndNote library with PDFs and folder structure, let me know!

#Linux#EndOf10#ResearchTools
Public *
Ronja

(1/X) A researcher (new to Linux, minimal time to learn) wants to switch from Microsoft. Main needs:
- Video calls
- Coding text docs
- Audio-to-text transcription
- Presentations
- Teaching + participation tools
- Video creation
- E-learning modules
- Simple photo/audio editing
Where can they find a good overview of Linux-compatible tools for research & education? Drop your recs 👇

#Linux#EndOf10#ResearchTools
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