Personal information

Scientific Knowledge Engineering

Biography

Gully is a research scientist at the Chan Zuckerberg Initiative Foundation. He develops scientific knowledge engineering capabilities within the CZIF Science Technology team. His work is centered on providing a bridge between the information technology under development, the biologists attempting to use it, and cutting-edge AI research to improve the core capabilities of the tech.

He previously ran the Scientific Knowledge Engineering group at USC's Information Sciences Institute. His work is centered on developing innovative methods to acquire, store, process and empower scientific knowledge primarily based on (but not limited to) the scientific literature.

Activities

Employment (6)

The Chan Zuckerberg Initiative: Redwood City, CA, US

2018-12-03 to present | Research Scientist (CZIF Science)
Employment
Source: Self-asserted source
Gully A Burns

Information Sciences Institute: Marina Del Rey, CA, US

2015-09-26 to 2018-11-30 | Research Lead (Intelligent Systems Division)
Employment
Source: Self-asserted source
Gully A Burns

Information Sciences Institute: Marina Del Rey, CA, US

2010-10-01 to 2015-09-25 | Project Leader (Intelligent Systems Division)
Employment
Source: Self-asserted source
Gully A Burns

Information Sciences Institute: Marina Del Rey, CA, US

2006-05-01 to 2010-01-01 | Research Neuroinformatics (Intelligent Systems Division)
Employment
Source: Self-asserted source
Gully A Burns

University of Southern California: Los Angeles, CA, US

2001-01-01 to 2006-04-30 | Research Assistant Professor (Neuroscience)
Employment
Source: Self-asserted source
Gully A Burns

University of Southern California: Los Angeles, CA, US

1997-08-01 to 2000-01-01 | Postdoc (Neuroscience )
Employment
Source: Self-asserted source
Gully A Burns

Education and qualifications (2)

Imperial College: London, GB

B.Sc. (Physics)
Education
Source: Self-asserted source
Gully A Burns

University of Oxford: Oxford, Oxfordshire, GB

1992-09-01 to 1997-09-01 | D.Phil. (Physiology)
Education
Source: Self-asserted source
Gully A Burns

Funding (6)

Evidence Extraction Systems for the Molecular Interaction Literature

Source: Self-asserted source
Gully A Burns via DimensionsWizard

Text Mining Infrastructure for the Entire Biological Literature

2009-09-01 to 2013-08-31 | Grant
National Science Foundation - Directorate for Biological Sciences (n/a, US)
GRANT_NUMBER: 0849977
Source: Self-asserted source
Gully A Burns via DimensionsWizard

Informatics Infrastructure for vector-based neuroanatomical atlases

Source: Self-asserted source
Gully A Burns via DimensionsWizard

NINDS MAP PHASE II: AN INFORMATICS TOOL FOR EVALUATING THE NINDS RESEARCH PORTFO

Source: Self-asserted source
Gully A Burns via DimensionsWizard

BioScholar: a Biomedical Knowledge Engineering framework based on the published l

Source: Self-asserted source
Gully A Burns via DimensionsWizard

KNOWLEDGE MANAGEMENT OF THE NEUROSCIENTIFIC LITERATURE

Source: Self-asserted source
Gully A Burns via DimensionsWizard

Works (50 of 54)

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Experiment Segmentation in Scientific Discourse as Clause-level Structured Prediction using Recurrent Neural Networks

CoRR
2017 | Journal article
Source: Self-asserted source
Gully A Burns

Molecular Interaction Evidence Fragment Corpus.

2017 | Other
Source: Self-asserted source
Gully A Burns

Extracting Evidence Fragments for Distant Supervision of Molecular Interactions

2017-09-23 | Preprint
Contributors: Gully A Burns; Pradeep Dasigi; Eduard H. Hovy
Source: check_circle
Crossref

Abstract Meaning Representations as Linked Data

The Semantic Web -- ISWC 2016: 15th International Semantic Web Conference, Kobe, Japan, October 17--21, 2016, Proceedings, Part II
2016 | Conference paper
Part of ISBN: 978-3-319-46547-0
Source: Self-asserted source
Gully A Burns

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections

Database (Oxford)
2016 | Journal article
Source: Self-asserted source
Gully A Burns

Curating Central Injection Studies from the Literature Using a General Purpose Knowledge Management Strategy

Annual Meeting for the Society for Neuroscience
2016 | Conference paper
Source: Self-asserted source
Gully A Burns

Cycles of Scientific Investigation in Discourse

Biocreative
2016 | Conference paper
Source: Self-asserted source
Gully A Burns

Modeling Concept Dependencies in a Scientific Corpus

Proceedings of the Annual Meeting of the Association for Computational Linguistics (ACL2016)
2016 | Conference paper
Source: Self-asserted source
Gully A Burns

SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading

PeerJ
2014 | Journal article
Source: Self-asserted source
Gully A Burns

‘Its All Made Up’ - Why we should stop building representations based on interpretive models and focus on experimental evidence instead

Discovery Informatics: Scientific Discoveries Enabled by AI
2014 | Conference paper
Source: Self-asserted source
Gully A Burns

Automatic Derivation of Topic Maps from Neuroscientific Publications

INCF 2013
2013 | Conference paper
Source: Self-asserted source
Gully A Burns

Finna: A Paragraph Prioritization System for Biocuration in the Neurosciences

Discovery Informatics Symposium DIS2013
2013 | Conference paper
Source: Self-asserted source
Gully A Burns

Supporting Document Triage with the SciKnowMine System in the Mouse Genome Informatics (MGI) Curation Process

Biocreative 4 Proceedings
2013 | Conference paper
Source: Self-asserted source
Gully A Burns

Virk: An Active Learning-based System for Bootstrapping Knowledge Base Development in the Neurosciences

Frontiers in Neuroinformatics
2013 | Journal article
Source: Self-asserted source
Gully A Burns

Towards structured sharing of raw and derived neuroimaging data across existing resources

Neuroimage
2013-11 | Journal article
Source: Self-asserted source
Gully A Burns

Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV)

Neuroimage
2013-05 | Journal article
Source: Self-asserted source
Gully A Burns

A lightweight Ontology Design Pattern to curate and represent experimental variables from vaccine protection studies.

Vacccine and Drug Ontology in the Study of Mechanism and Effect, ICBO 2012
2012 | Conference paper
Source: Self-asserted source
Gully A Burns

Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV)

Bio-Ontologies SIG, ISMB
2012 | Conference paper
Source: Self-asserted source
Gully A Burns

Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database

PLoS Genet.
2012 | Journal article
Source: Self-asserted source
Gully A Burns

Development of curation tools for making connections between observations and interpretations through experimental designs

Biocuration
2012 | Conference paper
Source: Self-asserted source
Gully A Burns

Layout-aware text extraction from full-text PDF of scientific articles

Source Code for Biology and Medicine
2012 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Modeling Neuroanatomical Spatial Data Using the Ontology of Experimental Variables and Values (OoEVV)

2012 | Conference paper
Source: Self-asserted source
Gully A Burns

Preliminary meta-analyses of experimental design with examples from HIV vaccine protection studies

Discovery Informatics Symposium DIS2012
2012 | Conference paper
Source: Self-asserted source
Gully A Burns

Text mining for the biocuration workflow

Database
2012 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Toward interoperable bioscience data

Nature Genetics
2012 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Database of NIH grants using machine-learned categories and graphical clustering

Nature Methods
2011 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Enabling collaborative research using the Biomedical Informatics Research Network (BIRN)

Journal of the American Medical Informatics Association
2011 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case

BMC Bioinformatics
2011 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Biomedical knowledge engineering tools based on experimental design: A case study based on neuroanatomical tract-tracing experiments

K-CAP'09 - Proceedings of the 5th International Conference on Knowledge Capture
2009 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

The NIH visual browser: An interactive visualization of biomedical research

Proceedings of the International Conference on Information Visualisation
2009 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier
grade
Preferred source (of 2)‎

An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006.

PLoS ONE
2008 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Intelligent approaches to mining the primary research literature: Techniques, systems, and examples

Studies in Computational Intelligence
2008 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Extracting data records from unstructured biomedical full text

EMNLP-CoNLL 2007 - Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning
2007 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Infrastructure for annotation-driven information extraction from the primary scientific literature: Principles and practice

Proceedings - 2007 IEEE Congress on Services, SERVICES 2007
2007 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

NeuroScholar's Electronic Laboratory Notebook and its application to neuroendocrinology

Neuroinformatics
2006 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

The NeuARt II system: A viewing tool for neuroanatomical data based on published neuroanatomical atlases

BMC Bioinformatics
2006 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

Journal of Biomedical Discovery and Collaboration
2006 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Projections from the subfornical region of the lateral hypothalamic area

Journal of Comparative Neurology
2005 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Tools and approaches for the construction of knowledge models from the neuroscientific literature

Neuroinformatics
2003 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Software engineering tools and approaches for neuroinformatics: The design and implementation of the View-Primitive Data Model framework (VPDMf)

Neurocomputing
2002 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac)

Philosophical Transactions of the Royal Society B: Biological Sciences
2001 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Knowledge management of the neuroscientific literature: The data model and underlying strategy of the NeuroScholar system

Philosophical Transactions of the Royal Society B: Biological Sciences
2001 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Knowledge Mechanics and the Neuroscholar Project

Source: Self-asserted source
Gully A Burns

The Neuroanatomical Rat Brain Viewer (NeuARt)

Source: Self-asserted source
Gully A Burns

Towards a federated neuroscientific knowledge management system using brain atlases

Neurocomputing
2001 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Analysis of the connectional organization of neural systems associated with the hippocampus in rats

Philosophical Transactions of the Royal Society B: Biological Sciences
2000 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat

Philosophical Transactions of the Royal Society B: Biological Sciences
2000 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Computational analysis of functional connectivity between areas of primate cerebral cortex

Philosophical Transactions of the Royal Society B: Biological Sciences
2000 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

Neuroscholar 1.00, A neuroinformatics databasing website

Neurocomputing
1999 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier

The connectional organization of the cortico-thalamic system of the cat

Cerebral Cortex
1999 | Journal article
Source: Self-asserted source
Gully A Burns via Scopus - Elsevier
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