Abstract:
BACKGROUND:The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore the grand theme, we extended the evaluation from a perspective of KB construction. Also, the Gene Regulation Ontology (GRO) task was newly introduced in the third edition. The final evaluation of the participating systems resulted in relatively low performance. The reason was attributed to the large size and complex semantic representation of the ontology. To investigate potential benefits of resource exchange between the presumably similar tasks, we measured the overlap between the datasets of the two tasks, and tested whether the dataset for one task can be used to enhance performance on the other. RESULTS:We report an extended evaluation on all the participating systems in the GE task, incoporating a KB perspective. For the evaluation, the final submission of each participant was converted to RDF statements, and evaluated using 8 queries that were formulated in SPARQL. The results suggest that the evaluation may be concluded differently between the two different perspectives, annotation vs. KB. We also provide a comparison of the GE and GRO tasks by converting their datasets into each other's format. More than 90% of the GE data could be converted into the GRO task format, while only half of the GRO data could be mapped to the GE task format. The imbalance in conversion indicates that the GRO is a comprehensive extension of the GE task ontology. We further used the converted GRO data as additional training data for the GE task, which helped improve GE task participant system performance. However, the converted GE data did not help GRO task participants, due to overfitting and the ontology gap.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Kim JD,Kim JJ,Han X,Rebholz-Schuhmann Ddoi
10.1186/1471-2105-16-S10-S3subject
Has Abstractpub_date
2015-01-01 00:00:00pages
S3issn
1471-2105pii
1471-2105-16-S10-S3journal_volume
16 Suppl 10pub_type
杂志文章abstract:BACKGROUND:The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-79
更新日期:2011-03-18 00:00:00
abstract:BACKGROUND:Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introd...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-256
更新日期:2013-08-22 00:00:00
abstract::We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...
journal_title:BMC bioinformatics
pub_type:
doi:10.1186/1471-2105-9-S1-S1
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plan...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-6
更新日期:2005-01-11 00:00:00
abstract:BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S11-S4
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-164
更新日期:2013-05-22 00:00:00
abstract:BACKGROUND:Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potential multimolecular complex. However, the tri-dimensional structure of urokinase, urokinase receptor a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S2-S8
更新日期:2008-03-26 00:00:00
abstract:BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1266-4
更新日期:2016-11-11 00:00:00
abstract:BACKGROUND:Lung adenocarcinoma is the most common type of lung cancer, with high mortality worldwide. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abundant data on gene expression, DNA methylation, and miRNA quantification. However, the hub genes, which...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2739-z
更新日期:2019-05-01 00:00:00
abstract:BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2272-5
更新日期:2018-08-13 00:00:00
abstract:BACKGROUND:Biologists often conduct multiple but different cDNA microarray studies that all target the same biological system or pathway. Within each study, replicate slides within repeated identical experiments are often produced. Pooling information across studies can help more accurately identify true target genes. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-247
更新日期:2006-05-05 00:00:00
abstract:BACKGROUND:Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-175
更新日期:2011-05-19 00:00:00
abstract:BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0611-3
更新日期:2015-05-22 00:00:00
abstract:BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-229
更新日期:2010-05-06 00:00:00
abstract:BACKGROUND:Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2362-4
更新日期:2018-09-26 00:00:00
abstract:BACKGROUND:The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel Dat...
journal_title:BMC bioinformatics
pub_type: 杂志文章,评审
doi:10.1186/1471-2105-5-3
更新日期:2004-01-09 00:00:00
abstract:BACKGROUND:The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-386
更新日期:2006-08-18 00:00:00
abstract:BACKGROUND:One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of stationary control policies. In large networks, it becomes computationally burdensome to derive an o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S10-S10
更新日期:2011-10-18 00:00:00
abstract::In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S19-S1
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1359-0
更新日期:2016-11-25 00:00:00
abstract:BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S2-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1938-8
更新日期:2017-11-21 00:00:00
abstract:BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1981-5
更新日期:2017-12-21 00:00:00
abstract:BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03777-y
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1499-x
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipeli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1592-1
更新日期:2017-03-20 00:00:00
abstract:BACKGROUND:Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S7
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-525
更新日期:2008-12-08 00:00:00
abstract:BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0480-9
更新日期:2015-02-19 00:00:00
abstract:BACKGROUND:The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. Whi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-203
更新日期:2007-06-14 00:00:00