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SourceData - a semantic platform for curating and searching figures [article]

Robin Liechti, Nancy George, Sara El-Gebali, Lou Götz, Isaac Crespo, Ioannis Xenarios, Thomas Lemberger
2016 bioRxiv   pre-print
SourceData focuses on the core of scientific evidence - data presented in figures - and makes papers searchable based on their data content.  ...  By coupling data availability to improved discoverability, SourceData aims at establishing a self-reinforcing data ′ecosystem′ that bridges the conventional visual and narrative description of research  ...  With SourceData, we provide an integrated platform that makes such data-oriented searches intuitive and efficient.  ... 
doi:10.1101/058529 fatcat:47qwc7sezzc53krln54wn2r4uu

SPRENO: a BioC module for identifying organism terms in figure captions

Hong-Jie Dai, Onkar Singh
2018 Database: The Journal of Biological Databases and Curation  
However, data as such is unacknowledged by machines as the descriptions in the figure captions comprise of sumptuous information in an ambiguous manner.  ...  This process is labor-intensive but indispensable to ensure the quality of the data.  ...  In addition, the frequent use of strain terms in the figure captions also makes the task even more challenging.  ... 
doi:10.1093/database/bay048 pmid:29873706 pmcid:PMC6007219 fatcat:leki4amzwrehrajfb56vrwugzy

Reproducibility will only come with data liberation

Mohammed AlQuraishi, Peter K. Sorger
2016 Science Translational Medicine  
Alas, this is not the case: The vast majority of preclinical, translational, and clinical research data are locked away in rasterized figures and non-text files that make reanalysis nearly impossible.  ...  Such problems could be studied and addressed much more effectively were the data in published papers and figures easily accessible for reanalysis.  ...  Why, then, do many biomedical research scientists resist the call to make primary data available in a discoverable and reusable form?  ... 
doi:10.1126/scitranslmed.aaf0968 pmid:27194726 pmcid:PMC5084089 fatcat:agksny6cyvfm7m5sirygomapvm

Biocuration: Distilling data into knowledge

2018 PLoS Biology  
The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to.  ...  Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data  ...  Understanding what makes data assets distinct from other types of assets is fundamental in terms of their valuation and effective management [2] .  ... 
doi:10.1371/journal.pbio.2002846 pmid:29659566 pmcid:PMC5919672 fatcat:7oq5p3avend43k2wfbdm3ksz6y

Navigating in vitro bioactivity data by investigating available resources using model compounds

Sten Ilmjärv, Fiona Augsburger, Jerven Tjalling Bolleman, Robin Liechti, Alan James Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
2019 Scientific Data  
the number of chemical compounds and associated experimental data in public databases is growing, but presently there is no simple way to access these data in a quick and synoptic manner.  ...  Instead, data are fragmented across different resources and interested parties need to invest invaluable time and effort to navigate these systems.  ...  Efforts similar to SourceData 9 , that allows to annotate already published figures in existing publication, and RepositiveIO (https://repositive.io/), that makes improving metadata a crowd-sourced task  ... 
doi:10.1038/s41597-019-0046-1 pmid:31036807 pmcid:PMC6488657 fatcat:xqctb3aslrghradq6phgocy5bu

Artificial intelligence-assisted tools for redefining the communication landscape of the scholarly world

Habeeb Ibrahim Abdul Razack, Sam T. Mathew, Fathinul Fikri Ahmad Saad, Saleh A. Alqahtani
2021 Science Editing  
Semantic tools may empower transparent and proficient data extraction tactics.  ...  It may help develop "smart publishers" by aiding humans to accomplish complex editorial tasks, such as analyzing large quantities of data, making predictions and forecasts, suggesting decisions based on  ...  ML can enhance post-publication discoverability by providing high precision recommendations [89] .  ... 
doi:10.6087/kcse.244 fatcat:ubbhruf26jbaxfixtczeovhqlq

Harmonizing the Metadata Among Diverse Climate Change Datasets

André Vellino
2015 International Journal of Digital Curation  
enhance the discoverability and reuse of data from a broad range of data sources.  ...  the human data integration process.  ...  Inconsistent practices for data sharing make each new data acquisition a time-consuming learning experience' (Richard et al., 2014) .  ... 
doi:10.2218/ijdc.v10i1.367 fatcat:esxdsntn6jcxvo3mflx5h3o3ym

The DocMaps Framework for representing assertions on research products in an extensible, machine-readable, and discoverable format [article]

Gary S McDowell, Jessica K Polka, Tony Ross-Hellauer, Gabriel Stein
2021 bioRxiv   pre-print
To support researchers in a world of experimentation in scholarly publishing, we propose a machine-readable, extensible, and discoverable framework for representing and surfacing review and editorial processes  ...  The aim is to give people the data they need to make those judgements.  ...  DocMaps would make more data about editorial processes accessible, allowing researchers to systematically study processes and because the data would be public and interoperable, this could be done repeatedly  ... 
doi:10.1101/2021.07.13.452204 fatcat:zsanpixrbbcrjcvkqi7bdbt24m

Harmonizing semantic annotations for computational models in biology

Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba (+16 others)
2018 Briefings in Bioinformatics  
Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent.  ...  These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores.  ...  Efforts such as the SourceData project [61] , which aims to make biological data discoverable through the use of metadata annotations, can help achieve this vision.  ... 
doi:10.1093/bib/bby087 pmid:30462164 fatcat:hn6gsuwefneunmk4hda6pn54zq

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

P. Gaudet, C. Arighi, F. Bastian, A. Bateman, J. A. Blake, M. J. Cherry, P. D'Eustachio, R. Finn, M. Giglio, L. Hirschman, R. Kania, W. Klimke (+16 others)
2012 Database: The Journal of Biological Databases and Curation  
Similarly, the EMBO SourceData project aims to integrate data and structured metadata into papers. These initiatives will help ensure that raw data are preserved, reusable and discoverable.  ...  The large number of available sequences in those species makes it very difficult for researchers to unambiguously describe the genes and proteins they are working on; therefore, efforts to integrate all  ... 
doi:10.1093/database/bas036 pmid:23110974 pmcid:PMC3483532 fatcat:v56fpejv3jftbo62gjdhjyswja

Harmonizing semantic annotations for computational models in biology [article]

Maxwell L Neal, Matthias König, David Nickerson, Goksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba (+17 others)
2018 bioRxiv   pre-print
Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent.  ...  These annotations help researchers find and repurpose models, accelerate model composition, and enable knowledge integration across model repositories and experimental data stores.  ...  Efforts such as the SourceData project 61 , which aims to make biological data discoverable through the use of metadata annotations, can help achieve this vision.  ... 
doi:10.1101/246470 fatcat:u6l2kxadrjaopnarlvz6psmclm

And They Were There-Reports of Meetings

Ramue K. Kubilius, Sever Bordeianu
2018 Against the Grain  
Lemberger of EMBO (the European Molecular Biology Organization) explained projects involving AI which are part of the emerging open science landscape -see http://www.embo.org/news/press-releases/2017/ sourcedata-is-making-data-discoverable  ...  They cannot afford to make the data from their research open to all because they need to be the first to exploit it in publications. In the last session Dr.  ...  Discoverability is central to resources being used. Connecting users to relevant reference content is a continuing challenge.  ... 
doi:10.7771/2380-176x.8017 fatcat:em46zjxkybffpjddfd42sijhle

Biocuration: Distilling data into knowledge [article]

International Society For Biocuration, Mais Ammari, Andrew Chatr Aryamontri, Helen Attrill, Ivan Erill, Et Al, Maryland Shared Open Access Repository
2022
The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to.  ...  Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data  ...  Understanding what makes data assets distinct from other types of assets is fundamental in terms of their valuation and effective management [2] .  ... 
doi:10.13016/m25bat-oo9p fatcat:4icdds2e5re4pgdtg2zebb324m

Object tracking in augmented reality remote access laboratories without fiducial markers

Mark Smith, Alexander Kist, Andrew Maxwell
2019
Understanding and interacting with the visual scene is controlled through Computer Vision algorithms, and are crucial in ensuring that the AR systems co-operate with the data discovered through the systems  ...  Computer vision systems attempt to make sense of the seemingly random data sets that make up a digital image.  ...  of locating homogeneous pixels making up any shaped object.  ... 
doi:10.26192/xsfe-4a84 fatcat:duqqwm25tnb45ne4c4iamaonei