Abstract:
BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL. RESULTS:Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types. CONCLUSION:Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl ADdoi
10.1186/1471-2105-12-6subject
Has Abstractpub_date
2011-01-05 00:00:00pages
6issn
1471-2105pii
1471-2105-12-6journal_volume
12pub_type
杂志文章abstract:BACKGROUND:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-395
更新日期:2010-07-23 00:00:00
abstract:BACKGROUND:Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1928-x
更新日期:2017-11-28 00:00:00
abstract:BACKGROUND:Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that only represent conservation. There is no general way to represent correlated mutation and incorporat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S2-S2
更新日期:2010-04-16 00:00:00
abstract:BACKGROUND:Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic cl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-63
更新日期:2008-01-28 00:00:00
abstract:BACKGROUND:Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. RESULTS:We pres...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-177
更新日期:2006-03-29 00:00:00
abstract:BACKGROUND:The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-316
更新日期:2011-08-02 00:00:00
abstract:BACKGROUND:Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modell...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2357-1
更新日期:2018-09-21 00:00:00
abstract:BACKGROUND:Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences followi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S2-S19
更新日期:2006-09-06 00:00:00
abstract:BACKGROUND:Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-310
更新日期:2008-07-15 00:00:00
abstract:BACKGROUND:Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent b...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S1-S12
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-142
更新日期:2008-03-06 00:00:00
abstract:BACKGROUND:Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic information. This raises the question whether it can be done with less ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2337-5
更新日期:2018-10-12 00:00:00
abstract:BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0807-6
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunolo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S1-S19
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. Finding cis-regulatory elements in higher eukaryote genomes, however, remains a challenge, as searching in the promoter regions of genes with ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-44
更新日期:2006-01-26 00:00:00
abstract:BACKGROUND:GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that G...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0773-z
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2920-4
更新日期:2019-06-11 00:00:00
abstract:BACKGROUND:It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-342
更新日期:2008-08-15 00:00:00
abstract:BACKGROUND:Direct in vivo investigation of human metabolism is complicated by the distinct metabolic functions of various sub-cellular organelles. Diverse micro-environments in different organelles may lead to distinct functions of the same protein and the use of different enzymes for the same metabolic reaction. To be...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-393
更新日期:2010-07-22 00:00:00
abstract:BACKGROUND:Numerous tools have been developed to predict the fitness effects (i.e., neutral, deleterious, or beneficial) of genetic variants on corresponding proteins. However, prediction in terms of whether a variant causes the variant bearing protein to lose the original function or gain new function is also needed f...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0781-z
更新日期:2015-10-30 00:00:00
abstract:BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0394-y
更新日期:2014-12-14 00:00:00
abstract:BACKGROUND:A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for all reactions in a dilution series. This method suffers from a serious problem: The resulting ra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03604-4
更新日期:2020-07-08 00:00:00
abstract:BACKGROUND:In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS:We developed ImproViser...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-207
更新日期:2014-06-19 00:00:00
abstract:BACKGROUND:In the biomedical domain, the desired information of a question (query) asked by biologists usually is a list of a certain type of entities covering different aspects that are related to the question, such as genes, proteins, diseases, mutations, etc. Hence it is important for a biomedical information retrie...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S5-S8
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a g...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2547-x
更新日期:2019-02-04 00:00:00
abstract:BACKGROUND:Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2964-5
更新日期:2019-06-28 00:00:00
abstract:BACKGROUND:Joint and individual variation explained (JIVE), distinct and common simultaneous component analysis (DISCO) and O2-PLS, a two-block (X-Y) latent variable regression method with an integral OSC filter can all be used for the integrated analysis of multiple data sets and decompose them in three terms: a low(e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1037-2
更新日期:2016-06-06 00:00:00
abstract:BACKGROUND:One of key issues in the post-genomic era is to assign functions to uncharacterized proteins. Since proteins seldom act alone; rather, they must interact with other biomolecular units to execute their functions. Thus, the functions of unknown proteins may be discovered through studying their interactions wit...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S1-S64
更新日期:2010-01-18 00:00:00
abstract:BACKGROUND:The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-cou...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-254
更新日期:2006-05-15 00:00:00
abstract:BACKGROUND:Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the N...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-381
更新日期:2011-09-27 00:00:00