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Article ; Online: A novel tool for standardizing clinical data in a semantically rich model

Hayden G. Freedman / Heather Williams / Mark A. Miller / David Birtwell / Danielle L. Mowery / Christian J. Stoeckert, Jr.

Journal of Biomedical Informatics: X, Vol 8, Iss , Pp 100086- (2020)

2020

Abstract: Standardizing clinical information in a semantically rich data model is useful for promoting interoperability and facilitating high quality research. Semantic Web technologies such as Resource Description Framework can be utilized to their full potential ...

Abstract	Standardizing clinical information in a semantically rich data model is useful for promoting interoperability and facilitating high quality research. Semantic Web technologies such as Resource Description Framework can be utilized to their full potential when a model accurately reflects the semantics of the clinical situation it describes. To this end, ontologies that abide by sound organizational principles can be used as the building blocks of a semantically rich model for the storage of clinical data. However, it is a challenge to programmatically define such a model and load data from disparate sources. The PennTURBO Semantic Engine is a tool developed at the University of Pennsylvania that transforms concise RDF data into a source-independent, semantically rich model. This system sources classes from an application ontology and specifically defines how instances of those classes may relate to each other. Additionally, the system defines and executes RDF data transformations by launching dynamically generated SPARQL update statements. The Semantic Engine was designed as a generalizable data standardization tool, and is able to work with various data models and incoming data sources. Its human-readable configuration files can easily be shared between institutions, providing the basis for collaboration on a standard data model.
Keywords	Clinical data ; Biomedical ontologies ; Common data model ; Data interoperability ; Semantic Web technologies ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	004
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Clustering of genes into regulons using integrated modeling-COGRIM

Chen, Guang / Christian J Stoeckert Jr / Shane T Jensen

Genome biology. 2007 Jan., v. 8, no. 1

2007

Abstract: We present a Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion. COGRIM was applied to both unicellular and mammalian ... ...

Abstract	We present a Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion. COGRIM was applied to both unicellular and mammalian organisms under different scenarios of available data. In these applications, we demonstrate the ability to predict gene-transcription factor interactions with reduced numbers of false-positive findings and to make predictions beyond what is obtained when single types of data are considered.
Keywords	gene expression ; mammals ; models ; prediction ; regulon ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2007-01
Size	p. 1486.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2007-8-1-r4
Database	NAL-Catalogue (AGRICOLA)

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Article: Promoter features related to tissue specificity as measured by Shannon entropy

Schug, Jonathan / Christian J Stoeckert Jr / Claudia Kappen / J Michael Salbaum / Maja Bucan / Winfried-Paul Schuller

Genome biology. 2005 Apr., v. 6, no. 4

2005

Abstract: BACKGROUND: The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys ... ...

Abstract	BACKGROUND: The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms. RESULTS: We introduce a definition of tissue specificity based on Shannon entropy to rank human genes according to their overall tissue specificity and by their specificity to particular tissues. We apply our definition to microarray-based and expressed sequence tag (EST)-based expression data for human genes and use similar data for mouse genes to validate our results. We show that most genes show statistically significant tissue-dependent variations in expression level. We find that the most tissue-specific genes typically have a TATA box, no CpG island, and often code for extracellular proteins. As expected, CpG islands are found in most of the least tissue-specific genes, which often code for proteins located in the nucleus or mitochondrion. The class of genes with no CpG island or TATA box are the most common mid-specificity genes and commonly code for proteins located in a membrane. Sp1 was found to be a weak indicator of less-specific expression. YY1 binding sites, either as initiators or as downstream sites, were strongly associated with the least-specific genes. CONCLUSIONS: We have begun to understand the components of promoters that distinguish tissue-specific from ubiquitous genes, to identify associations that can predict the broad class of gene expression from sequence data alone.
Keywords	binding sites ; entropy ; expressed sequence tags ; gene expression ; genes ; genomic islands ; humans ; mice ; microarray technology ; mitochondria ; proteins ; surveys ; TATA box
Language	English
Dates of publication	2005-04
Size	p. 1068.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2005-6-4-r33
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Article: ApiDB: integrated resources for the apicomplexan bioinformatics resource center

Aurrecoechea, Cristina / Heiges, Mark / Wang, Haiming / Wang, Zhiming / Fischer, Steve / Rhodes, Philippa / Miller, John / Kraemer, Eileen / Stoeckert, Christian J. Jr / Roos, David S / Kissinger, Jessica C

Nucleic acids research. 2007 Jan., v. 35, no. suppl_1

2007

Abstract: ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and ... ...

Abstract	ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and TOXOPLASMA: ApiDB serves not only as a database in its own right, but as a single web-based point of entry that unifies access to three major existing individual organism databases (PlasmoDB.org, ToxoDB.org and CryptoDB.org), and integrates these databases with data available from additional sources. Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases.
Keywords	Cryptosporidium ; Internet ; Plasmodium ; Protozoa ; Toxoplasma ; bioinformatics ; databases ; humans ; nucleic acids
Language	English
Dates of publication	2007-01
Size	p. D427-D430.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes

Mazzarelli, Joan M / Brestelli, John / Gorski, Regina K / Liu, Junmin / Manduchi, Elisabetta / Pinney, Deborah F / Schug, Jonathan / White, Peter / Kaestner, Klaus H / Stoeckert, Christian J. Jr

Nucleic acids research. 2007 Jan., v. 35, no. suppl_1

2007

Abstract: EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression ... ...

Abstract	EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.
Keywords	binding sites ; data collection ; databases ; diabetes ; gene expression ; genes ; genetic models ; islets of Langerhans ; microarray technology ; nucleic acids ; promoter regions ; reverse transcriptase polymerase chain reaction ; tissues ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2007-01
Size	p. D751-D755.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: ToxoDB: an integrated Toxoplasma gondii database resource

Gajria, Bindu / Bahl, Amit / Brestelli, John / Dommer, Jennifer / Fischer, Steve / Gao, Xin / Heiges, Mark / Iodice, John / Kissinger, Jessica C / Mackey, Aaron J / Pinney, Deborah F / Roos, David S / Stoeckert, Christian J. Jr / Wang, Haiming / Brunk, Brian P

Nucleic acids research. 2008 Jan., v. 36, no. suppl_1

2008

Abstract: ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, ... ...

Abstract	ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website.
Keywords	Internet ; Protozoa ; Toxoplasma gondii ; databases ; expressed sequence tags ; gene expression ; genome ; nucleic acids ; parasites ; proteomics
Language	English
Dates of publication	2008-01
Size	p. D553-D556.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database

Zhu, Yunxia / Babak Parvizi / Benjamin L King / Brian P Brunk / Carol J Bult / Christian J Stoeckert Jr / Joel Richardson / John Quackenbush

Genome biology. 2003 Feb., v. 4, no. 2

2003

Abstract: Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such ... ...

Abstract	Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such biological information as genomic location, gene function, gene expression and phenotypic variation. We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database.
Keywords	databases ; gene expression ; genes ; genomics ; mice ; phenotypic variation ; sequence analysis
Language	English
Dates of publication	2003-02
Size	p. 526.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2003-4-2-r16
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Article: AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

Aurrecoechea, Cristina / Barreto, Ana / Brestelli, John / Brunk, Brian P / Caler, Elisabet V / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen T / Li, Wei / Nayak, Vishal / Pennington, Cary / Pinney, Deborah F /

Pitts, Brian / Roos, David S / Srinivasamoorthy, Ganesh / Stoeckert, Christian J. Jr / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2011 Jan., v. 39, no. suppl_1

2011

Abstract: AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. ... ...

Abstract	AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.
Keywords	Amoebozoa ; Encephalitozoon cuniculi ; Entamoeba ; bioinformatics ; expressed sequence tags ; genes ; genetic databases ; hypersensitivity ; infectious diseases ; microarray technology ; nucleic acids ; phylogeny ; protein synthesis
Language	English
Dates of publication	2011-01
Size	p. D612-D619.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: EuPathDB: a portal to eukaryotic pathogen databases

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen T / Li, Wei / Miller, John A / Nayak, Vishal / Pennington, Cary / Pinney, Deborah F /

Roos, David S / Ross, Chris / Srinivasamoorthy, Ganesh / Stoeckert, Christian J. Jr / Thibodeau, Ryan / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2010 Jan., v. 38, no. suppl_1

2010

Abstract: EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and TRYPANOSOMA: While each of these groups is ... ...

Abstract	EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and TRYPANOSOMA: While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently-implemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
Keywords	Cryptosporidium ; Giardia ; Leishmania ; Neospora ; Plasmodium ; Toxoplasma ; Trichomonas ; Trypanosoma ; databases ; infrastructure ; nucleic acids ; pathogens ; user interface
Language	English
Dates of publication	2010-01
Size	p. D415-D419.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: PlasmoDB: a functional genomic database for malaria parasites

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P / Dommer, Jennifer / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen / Li, Wei / Miller, John A / Nayak, Vishal / Pennington, Cary /

Pinney, Deborah F / Roos, David S / Ross, Chris / Stoeckert, Christian J. Jr / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2009 Jan., v. 37, no. suppl_1

2009

Abstract: PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed ... ...

Abstract	PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
Keywords	Plasmodium ; bioinformatics ; evolution ; genome ; malaria ; menu planning ; nucleic acids ; parasites ; proteomics ; transcription (genetics)
Language	English
Dates of publication	2009-01
Size	p. D539-D543.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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