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Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation

Amit Gupta, Weijia Xu, Pankaj Jaiswal, Crispin Taylor, Jennifer Regala
2018 International Conference on Biomedical Ontology  
We will present updates on an ongoing project DIVE (Domain Informational Vocabulary Extraction), a system designed for extracting domain information from scientific publications.  ...  We also discuss our experiences from successful integration of DIVE with the publishing pipeline for two prominent Plant Biology Journals (The Plant Cell and Plant Physiology ) from ASPB (American Society  ...  ACKNOWLEDGEMENTS DIVE is partially supported by CyVerse (NSF awards DBI0735191, DBI1265383) and by Gramene, A Comparative Plant Genomics Database (NSF award IOS 1127112).  ... 
dblp:conf/icbo/GuptaXJTR18 fatcat:4ctwu7meefgkxjkx3coztavbui

Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service

Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart, Jennifer Regala
2019 Data and Information Management  
In this paper, we present domain informational vocabulary extraction (DIVE) project, which aims to enrich digital publications through detection of entity and key informational words and by adding additional  ...  These extracted entities are then stored in a database and made accessible through an interactive web application for curation and evaluation by authors.  ...  Acknowledgements: This research is partially supported by CyVerse (NSF awards DBI-0735191 and DBI-1265383) and Gramene, a comparative plant genomics database (NSF award IOS-1127112).  ... 
doi:10.2478/dim-2019-0003 fatcat:w4swautdkbefti3gfy4scsle5u

FREYA Guest Webinar: CoronaWhy Knowlegde Graph

Vyacheslav Tykhonov, Ricarda Braukmann
2020 Zenodo  
This upload consists of the presentations and the video recording from the FREYA guest webinar on the CoronaWhy Knowlegde Graph. The webinar was held on Tuesday 1st of September 2020 at 16:00 CEST  ...  21 Challenge of data integration and various ontologies CORD-19 collection processing with NLP pipeline: • manual annotation and labelling of COVID-19 related papers • automatic entity extraction and classification  ...  AI pipeline does domain specific entities extraction and ranking of relevant CORD-19 papers. 2.  ... 
doi:10.5281/zenodo.4010843 fatcat:ctc5cdk6rbhqngakdgv4u2xnki

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Daniela Raciti, Karen Yook, Todd W Harris, Tim Schedl, Paul W Sternberg
2018 Database: The Journal of Biological Databases and Curation  
While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations  ...  Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases  ...  Acknowledgements The authors would like to thank members of the C. elegans research community and representatives from other model organisms databases such as TAIR (The Arabidopsis Information Resource  ... 
doi:10.1093/database/bay013 pmid:29688367 pmcid:PMC5836261 fatcat:dhf2ampq4jgjzkpwnb7g63xkh4

BIM: an open ontology for the annotation of biomedical images

Ahmad C. Bukhari, Mate Levente Nagy, Michael Krauthammer, Paolo Ciccarese, Christopher J. O. Baker
2015 International Conference on Biomedical Ontology  
The BIM ontology provides semantic vocabularies to describe the manually curated image annotations as well as annotations gener-ated by online bioinformatics services using content extracted from images  ...  The BIM ontology is represented in three parts; (i) image vocabularies --which holds vocabularies for the annotation of an image and/or region of interests (ROI) inside an image, as well as vocabularies  ...  This simple reference model makes it possible to integrate the extracted information semantically.  ... 
dblp:conf/icbo/BukhariNKCB15 fatcat:kfrvqdncxrhtlonwbt4jbjslu4

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
2015 Database: The Journal of Biological Databases and Curation  
Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially  ...  NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.  ...  We additionally thank the researchers, who deposit experimental data for public use. The authors are grateful for the comments and valuable recommendations from two anonymous reviewers.  ... 
doi:10.1093/database/bav099 pmid:26475471 pmcid:PMC4608514 fatcat:r5sachf3wjhqzcgb6lycqo6gre

Towards Evaluating the Impact of Semantic Support for Curating the Fungus Scientic Literature

Marie-Jean Meurs, Caitlin Murphy, Nona Naderi, Ingo Morgenstern, Carolina Cantu, Shary Semarjit, Greg Butler, Justin Powlowski, Adrian Tsang, René Witte
2011 Canadian Semantic Web Symposium  
Working closely with biologists who manually curate the existing literature, we developed ontological NLP pipelines, integrated through Web-based interfaces, to help them in two main tasks: spending less  ...  time to mine the literature for facts, while also being provided with richer and semantically linked information.  ...  Funding for this work was provided by Genome Canada and Génome Québec.  ... 
dblp:conf/csws/MeursMNMCSBPTW11 fatcat:2tauyrqv35foljmzhh7c5mj66u

Linked data for potential algal biomass production

Monika Solanki, Johannes Skarka, Craig Chapman
2013 Semantic Web Journal  
LEAPS forms the basis of a prototype Web application that enables stakeholders in the algal biomass domain to interactively explore via various facets, potential algal production sites and sources of their  ...  In this paper we present an account of the publication of a suite of datasets, LEAPS, that collectively enable the evaluation of potential algal biomass production sites in North West Europe (NWE).  ...  Datasets and vocabularies related to harvesting strategies and extraction techniques are the key semantic outputs of this stage.  ... 
doi:10.3233/sw-130105 fatcat:iwyenuxqb5gxza2qc56th5cqqu

Data management and best practice for plant science

Sabina Leonelli, Robert P. Davey, Elizabeth Arnaud, Geraint Parry, Ruth Bastow
2017 Nature Plants  
For instance, the Crop Ontology [14, 21] project works with communities of practice centred on a specific crop to develop and curate list of controlled vocabularies for crop traits along with an associated  ...  Furthermore, Crop Ontology facilitates data re-use by intersecting with existing data annotation pipelines such as the Integrated Breeding Platform [16] , and is accessible in the emerging agronomic ontology  ... 
doi:10.1038/nplants.2017.86 pmid:28585570 fatcat:5r4ymlczc5bq5mrnqgdkrgsb4u

The Gene Ontology (GO) project in 2006

2006 Nucleic Acids Research  
The Gene Ontology (GO) project (http://www. develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see  ...  A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository.  ...  ACKNOWLEDGEMENTS The Gene Ontology Consortium is supported by NIH/NHGRI grant HG02273 and has been supported by grants from the European Union RTD Programme 'Quality of Life and Management of Living Resources  ... 
doi:10.1093/nar/gkj021 pmid:16381878 pmcid:PMC1347384 fatcat:t4dm7drqvjcttkeiakru2iftia

14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations [article]

Federica Quaglia
2021 Zenodo  
booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations  ...  Conserved Domain Database (CDD) curators selected candidate models, refined pre-computed alignments, and abstracted functional information.  ...  Where possible, we are harmonizing existing MOD specific controlled vocabularies and working to get these terms incorporated in public ontologies.  ... 
doi:10.5281/zenodo.5570276 fatcat:nlbkkzkhfvhdddqu4ypzh247iy

Automatic Construction of a Semantic Knowledge Base from CEUR Workshop Proceedings [chapter]

Bahar Sateli, René Witte
2015 Communications in Computer and Information Science  
Our proposed solution is composed of two subsystems: (i) A text mining pipeline, developed based on the GATE framework, which extracts structural and semantic entities, such as authors' information and  ...  The output of our system is an RDF graph stored in a scalable TDB-based storage with a public SPARQL endpoint for the task's queries.  ...  Publication Ontology (PUBO).  ... 
doi:10.1007/978-3-319-25518-7_11 fatcat:sjrbad3zbbedjlvvnaxgyffad4

Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress

G. Mukherjee
2005 Plant Physiology  
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data.  ...  It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis  ...  A further development will be the design and implementation of an Ontology Manager tool that will allow the full integration of external ontologies and controlled vocabularies and also allow their terms  ... 
doi:10.1104/pp.105.063156 pmid:16219923 pmcid:PMC1255982 fatcat:ylj2obzlzjho7pratwpr2btcba

Uniform standards for genome databases in forest and fruit trees

J. L. Wegrzyn, D. Main, B. Figueroa, M. Choi, J. Yu, D. B. Neale, S. Jung, T. Lee, M. Stanton, P. Zheng, S. Ficklin, I. Cho (+8 others)
2012 Tree Genetics & Genomes  
ontologies to improve the extraction and exchange of the data for comparative analysis.  ...  This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted  ...  Gene Ontology and Plant Ontology have been well integrated into the functional annotation pipelines used by TreeGenes and tfGDR.  ... 
doi:10.1007/s11295-012-0494-7 fatcat:uvc6tk3mf5bzjbmqmkb6an3zqi

Methodology for FNS data standardisation and interoperability

Tome Eftimov, Panče Panov, Blaž Škrlj, Duccio Cavalieri, Francesco Vitali, Giovanni Bacci, Karl Presser, Agnieszka Matuszczak, Julia Kurps, Chris Evelo, Susan Coort
2020 Zenodo  
Moreover, existing resources and tools have been identified and included.  ...  In the selection and development of the methodology, the needs of the FNS project, especially of the use cases and demonstrators,were considered.  ...  In the next steps, we will first align the extracted terms with the BFO ontology and then integrate them with domain terms from the domain ontologies based on BFO, such asFoodOn and ONS, at the first instance  ... 
doi:10.5281/zenodo.6966439 fatcat:3a7v4chlevak5c7kqtgq4yf5cq
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