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Have you authored a C. elegans paper and want to contribute to community curation? Access our Author Curation Portal to participate.

The Author Curation to Knowledgebase project (ACKnowledge) aims at facilitating author curation to biological knowledgebases.

Biological knowledgebases serve as a critical resource for researchers and accelerate scientific discoveries by providing manually curated, machine-readable data collections. At present, the aggregation and manual curation of biological data is a labor-intensive process that relies almost entirely on professional biocurators. Biocuration, however, is greatly aided when authors directly participate in the process.

ACKnowledge employs a semi-automated curation pipeline that identifies biological entities and data types (for example, genes and anatomic expression) from newly published research articles and then automatically emails authors to review the extracted information through a dedicated web interface. During the curation process, authors may modify extracted data, an important quality control measure. Participating authors are publicly acknowledged for their contribution in the knowledgebase.

The ACKnowledge system, currently implemented by WormBase for the C. elegans literature and soon to be implemented for other species, couples statistical methods and state-of-the-art text mining algorithms to identify entities and data types.

Additional tools in the ACKnowledge system include software to send automated reminder emails to authors who have not completed their submissions, a notification system to inform knowledgebase curators about new author submissions, and a dashboard for curators to monitor submission status.

The ACKnowledge project is supported by grant R01 OD023041 from the National Library of Medicine at the US National Institutes of Health.

If you have questions about the ACKnowledge project, please contact help.acknowledge@wormbase.org.

ACKnowledge Github repository

Release Notes

Version 5.0

Release date

02-11-2025

Introduction

ACKnowledge 5.0 is a landmark update that brings advanced functionality and significant improvements to our system. This release aligns our data access infrastructure with the Alliance of Genome Resources (Alliance) central repository. By leveraging the Alliance, we can now seamlessly fetch PDFs and related bibliographic data, ensuring our users have access to the most comprehensive and up-to-date resources.

ACKnowledge 5.0 also introduces an enhanced backend architecture capable of extracting entities for multiple organisms. This new modularity allows us to fetch entity lists directly from the Alliance, broadening our scope and making our platform more versatile for diverse research needs.

The release also brings new features, performance improvements, and crucial bug fixes, all designed to provide a more robust and efficient user experience.

Main Updates

User Updates

Bug Fixes

Curator Dashboard Updates

Version 4.0

Release date

10-27-2022

Introduction

Release 4.0 marks an exciting transition for our project. With support from the National Library of Medicine, the Author First Pass (AFP) project is now officially known as ACKnowledge (Author Curation to Knowledgebase). This change reflects our commitment to expanding artificial intelligence (AI)-enhanced community curation to capture more detailed experimental findings and to introduce our curation pipeline to additional model organism communities and their respective knowledgebases. While busy transitioning our project and enhancing our AI methods, we also implemented further improvements to the current pipeline based on continuing valuable feedback from authors. These improvements, listed below, will help authors add more information about their papers and readily find previously published papers processed by our pipeline for curation using our Author Curation Portal.

Main Updates

User Updates

Bug Fixes

Curator Dashboard Updates

Version 3.0

Release Date

09-16-2021

Introduction

Based on valuable user feedback, we continue to improve the ACKnowledge experience. In addition to providing more streamlined ways to enter entities, we’ve added further instructions for adding new entities, and a link to look up specific entities in WormBase. We now flag papers for enzymatic activity and include a free-text field to describe other gene functions. We updated the FAQs and provide a link to the ACKnowledge webinar presented in February 2021. Lastly, to thank authors for their valuable contributions, we now acknowledge authors on WormBase person and paper pages.

We have implemented updates and improvements to our curator dashboard. The dashboard is a tool available to WormBase curators to keep track of submissions and perform quality control of submitted data.

Main Features

User Updates

Curator Dashboard Updates

Version 2.0

Release Date

09-14-2020

Introduction

We improved the ACKnowledge system based on feedback received from authors and statistics collected during one year of ACKnowledge v1.0 author submissions. We improved the definition of data types in the form and we refined our text mining algorithms to obtain better results.

Main Features

Version 1.0

Release date

06-03-2019

Introduction

We are proud to introduce our new ACKnowledge system, which leverages text mining to help authors curate their papers and send data to WormBase! The system replaces the previous form which required authors to submit data manually through free-text forms.

Main Features

References

[1] Arnaboldi V, Raciti D, Van Auken K, Chan JN, Muller H-M, Sternberg PW (2020) Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. Database, doi:10.1093/database/baaa006