Hilmar Lapp

Assistant Director for Informatics

National Evolutionary Synthesis Center (NESCent)

Location
Durham, North Carolina, United States
Discipline
Biological Sciences
Interests
Reusable and interoperable software, data, and semantics; Large-scale data integration; Cyberinfrastructure for biology; Building sustainable communities
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About

My research interests are in reusable and interoperable software and data, large-scale data integration, and in building open, sustainable eScience infrastructure. I am a biologist by training, but I have also more than two decades worth of experience developing various informatics tools and resources, ranging from commercial applications to real-time scientific data acquisition software, to bioinformatics data integration systems, standards, and ontologies.

At NESCent, I am involved with and have helped initiate many of the Center’s cyberinfrastructure initiatives aimed at grass-roots building of community capacity. I brought the hackathon program and Google Summer of Code participation to the Center. I am co-PI of the NSF-funded Phenoscape project (http://phenoscape.org) on ontological annotation of evolutionary phenotype observations, co-convener of the Biodiversity Information Standards (TDWG) Interest Group on Phylogenetics Standards, senior personnel in the Dryad digital data repository for data supporting scientific publications (http://datadryad.org), and a participant in the Data Integration and Semantics Working Group of DataONE (http://dataone.org). Before joining NESCent, I worked for almost 10 years in functional genome informatics in the biopharmaceutical sector, where among other things I built SymAtlas, one of the first decidedly gene-centric database integrating genome annotation databases with gene function data.

I have also been been a long-time advocate of open-source and open development of software. Software I write is free for everyone to reuse, modify, and redistribute. I feel strongly that the open sharing and reuse of all scholarly inputs and outputs is key to accelerating the progress and long-time impact of science, and that the scholarly communication process works best if conducted as openly as possible. I aspire to practice these principles whenever I can, including publishing in open-access journals, and signing my peer reviews, whether positive or negative.
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Publications

  • BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

    Katayama T, Wilkinson M, Aoki-Kinoshita K, Kawashima S, Yamamoto Y, Yamaguchi A et al.

    Journal of biomedical semantics (2014)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • What is an anatomy ontology?

    Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P

    Anatomical Record (Hoboken, N.J. : 2007) (2013)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Response to GBIF request for consultation on data licenses

    Rees J, Cranston K, Lapp H, Vision T

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The Bioinformatics Open Source Conference (BOSC) 2013

    Harris N, Cock P, Chapman B, Goecks J, Hotz H, Lapp H

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

    Midford P, Dececchi T, Balhoff J, Dahdul W, Ibrahim N, Lapp H et al.

    Journal of Biomedical Semantics (2013)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Data from: A unified anatomy ontology of the vertebrate skeletal system

    Dahdul W, Balhoff J, Blackburn D, Diehl A, Haendel M, Hall B et al.

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • A grassroots approach to software sustainability

    Cranston K, O'Meara B, Lapp H, Vision T

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Software Engineering as Instrumentation for the Long Tail of Scientific Software

    Huang D, Lapp H

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Integrating anatomy and phenotype ontologies with taxonomic hierarchies

    Balhoff J, Midford P, Lapp H

    ICBO: International Conference on Biomedical Ontology (2011) Proceedings (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

    Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek C et al.

    BMC Bioinformatics (2013)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem

    Rodrigo A, Alberts S, Cranston K, Kingsolver J, Lapp H, McClain C et al.

    PLoS Biology (2013)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • A Unified Anatomy Ontology of the Vertebrate Skeletal System

    Dahdul W, Balhoff J, Blackburn D, Diehl A, Haendel M, Hall B et al.

    PLoS ONE (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The PLOS Computational Biology Software Section

    Prlić A, Lapp H

    PLoS Computational Biology (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011

    Robbins R, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D et al.

    Standards in Genomic Sciences (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

    Mabee P, Balhoff J, Dahdul W, Lapp H, Midford P, Vision T et al.

    Journal of Applied Ichthyology (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

    Vos R, Balhoff J, Caravas J, Holder M, Lapp H, Maddison W et al.

    Systematic biology (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

    Jung S, Menda N, Redmond S, Buels R, Friesen M, Bendana Y et al.

    Database (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Similarity between semantic description sets: addressing needs beyond data integration

    Vision T, Blake J, Lapp H, Mabee P, Westerfield M

    Proceedings of the First International Workshop on Linked Science (LISC 2011) (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Overview of FEED, the Feeding Experiments End-user Database.

    Wall C, Vinyard C, Williams S, Gapeyev V, Liu X, Lapp H et al.

    Integrative and Comparative Biology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Organizing our knowledge of biodiversity

    Lapp H, Morris R, Catapano T, Hobern D, Morrison N

    Bulletin of the American Society for Information Science and Technology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Meeting Report: BioSharing at ISMB 2010

    Field D, Sansone S, DeLong E, Sterk P, Friedberg I, Gaudet P et al.

    Standards in Genomic Sciences (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

    Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita K, Yamamoto Y et al.

    Journal of Biomedical Semantics (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

    Dahdul W, Balhoff J, Engeman J, Grande T, Hilton E, Kothari C et al.

    PLoS ONE (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Molecular classification of human carcinomas by use of gene expression signatures.

    Su A, Welsh J, Sapinoso L, Kern S, Dimitrov P, Lapp H et al.

    Cancer research (2001)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Exploring Trafficking GTPase Function by mRNA Expression Profiling: Use of the SymAtlas Web‐Application and the Membrome Datasets

    Gurkan C, Lapp H, Hogenesch J, Balch W

    Methods in Enzymology (2005)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Phenex: Ontological Annotation of Phenotypic Diversity

    Balhoff J, Dahdul W, Kothari C, Lapp H, Lundberg J, Mabee P et al.

    PLoS ONE (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The teleost anatomy ontology: anatomical representation for the genomics age.

    Dahdul W, Lundberg J, Midford P, Balhoff J, Lapp H, Vision T et al.

    Systematic Biology (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Linking big: the continuing promise of evolutionary synthesis.

    Sidlauskas B, Ganapathy G, Hazkani-Covo E, Jenkins K, Lapp H, McCall L et al.

    Evolution; International Journal of Organic Evolution (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Data and animal management software for large-scale phenotype screening.

    Ching K, Cooke M, Tarantino L, Lapp H

    Mammalian Genome (2006)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Large-scale profiling of Rab GTPase trafficking networks: the membrome.

    Gurkan C, Lapp H, Alory C, Su A, Hogenesch J, Balch W

    Molecular Biology of the Cell (2005)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Robust DNA microarray image analysis

    Brändle N, Bischof H, Lapp H

    Machine Vision and Applications (2003)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Applications of a rat multiple tissue gene expression data set.

    Walker J, Su A, Self D, Hogenesch J, Lapp H, Maier R et al.

    Genome research (2004)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • A gene atlas of the mouse and human protein-encoding transcriptomes.

    Su A, Wiltshire T, Batalov S, Lapp H, Ching K, Block D et al.

    Proceedings of the National Academy of Sciences of the United States of America (2004)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The Primate Life History Database: a unique shared ecological data resource

    Strier K, Altmann J, Brockman D, Bronikowski A, Cords M, Fedigan L et al.

    Methods in Ecology and Evolution (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The 2006 NESCent Phyloinformatics Hackathon: A Field Report

    Lapp H, Bala S, Balhoff J, Bouck A, Goto N, Holder M et al.

    Evolutionary Bioinformatics Online (2007)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Open source tools and toolkits for bioinformatics: significance, and where are we?

    Stajich J, Lapp H

    Briefings in Bioinformatics (2006)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Robust Parametric and Semi-parametric Spot Fitting for Spot Array Images

    Brändle N, Chen H, Bischof H, Lapp H

    Proc Int Conf Intell Syst Mol Biol (2000)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The Bioperl toolkit: Perl modules for the life sciences.

    Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C et al.

    Genome Research (2002)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.

Professional experience

Assistant Director for Informatics

National Evolutionary Synthesis Center (NESCent)

May 2006 - Present

Member, Board of Directors

Open Bioinformatics Foundation (OBF)

Present

Member, Organizing Committee

iEvoBio

Present

President

Open Bioinformatics Foundation (OBF)

Present

Bioinformatics Group Leader

Genomics Institute of the Novartis Research Foundation

September 2001 - April 2006 (4 years 7 months)

Bioinformatics Research Associate and Lab Head, Computational Biology & Data Mining

Novartis Research Institute

May 1997 - July 2001 (4 years 2 months)

Education history

Institute of Biology II, Albert-Ludwigs-University Freiburg

Dipl. Biology (M.Sc.)

October 1988 - January 1997 (8 years 3 months)

Department of Biology, Lüdwig-Maximilians University Munich

Vordiplom (BS)

September 1985 - June 1987 (1 year 9 months)