bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processing of natural language queries to a relational database
Authors: Samsonova M. , Pisarev A. , Blagov M. 
Published: July 2003

Abstract
Motivation: A new method is developed to query a relational database in natural language (NL).
Results: The method, based on a semantic approach, interprets grammatical and lexical units of a natural language into concepts of subject domain, which are given in a conceptual scheme. The conceptual scheme is mapped formally onto the logical scheme. We applied the method to query the FlyEx database in natural language. FlyEx contains information on the expression of segmentation genes in Drosophila melanogaster. The method allows formulation of queries in various natural languages simultaneously, and is adaptive to changes in the knowledge domain and user’s views. It provides optimal transformation of queries from natural language to SQL, as well as visualization of information as a hyperscheme. The method does not require specification of all possible language constructions as well as a standard grammar accuracy in formulation of NL queries.
Availability: http://urchin.spbcas.ru/NLP/NLP.html
Contact: samson@spbcas.ru
Keywords: natural language processing, relational databases, conceptual scheme, segmentation genes, D.melanogaster, query optimization.
*To whom correspondence should be addressed.
A tool to assist the study of specific
features at protein binding sites
Authors: Santander Víctor , Portales Miguel Angel , Melo Francisco 
Published: July 2003

Abstract
The Protein Data Bank contains a large amount of proteins that have been solved with small ligands bound to them. This constitutes a rich source of information for the study of the specific requirements of protein sites to bind small molecules with a favorable free energy. The specific atomic composition and three-dimensional geometric restraints of protein binding sites for different ligands could be easily obtained from there. The development of accurate binding site descriptors in proteins constitutes a valuable tool to assist in the large-scale prediction and annotation of protein function in whole genomes. In this work, an integrated database containing some processed and calculated protein/ligand information is described. It is expected that this database will constitute a useful tool for people working in the prediction of protein function from its structure. The database is accessible from the Internet through a web server located at: http://protein.bio.puc.cl
Contact: fmelo@genes.bio.puc.cl
Keywords: Ligands, function, structure, proteins, binding sites, conformational analysis
*To whom correspondence should be addressed.
STRUCLA: a WWW meta-server for protein structure comparison and
evolutionary classification
Authors: Sasin Joanna M. , Kurowski Michal A. , Bujnicki Janusz M. 
Published: July 2003

Abstract
Motivation: Evolutionary relationships of proteins have long been derived from the alignment of protein sequences. But from the view of function, most restraints of evolutionary divergence operate at the level of tertiary structure. It has been demonstrated that quantitative measures of dissimilarity in families of structurally similar proteins can be applied to the construction of trees from a comparison of their three-dimensional structures. However, no convenient tool is publicly available to carry out such analyses.
Results: We developed STRUCLA (STRUcture CLAssification), a WWW tool for generation of trees based on evolutionary distances inferred from protein structures according to various methods. The server takes as an input a list of PDB files or the initial alignment of protein coordinates provided by the user (for instance exported from SWISS PDB VIEWER). The user specifies the distance cutoff and selects the distance measures. The server returns series of unrooted trees in the NEXUS format and corresponding distance matrices, as well as a consensus tree. The results can be used as an alternative and a complement to a fixed hierarchy of current protein structure databases. It can complement sequence-based phylogenetic analysis in the ‘twilight zone of homology’, where amino acid sequences are too diverged to provide reliable relationships.
Availability: The service is free for all users and available at http://asia.genesilico.pl/strucla/
Contact: asia@genesilico.pl; iamb@genesilico.pl
*To whom correspondence should be addressed.
Discovering molecular pathways from protein interaction
and gene expression data
Authors: Segal E. , Wang H. , Koller D. 
Published: July 2003

Abstract
In this paper, we describe an approach for identifying‘ pathways’ from gene expression and protein interaction data. Our approach is based on the assumption that many pathways exhibit two properties: their genes exhibit a similar gene expression profile, and the protein products of the genes often interact. Our approach is based on a unified probabilistic model, which is learned from the data using the EM algorithm. We present results on two Saccharomyces cerevisiae gene expression data sets, combined with a binary protein interaction data set. Our results show that our approach is much more successful than other approaches at discovering both coherent functional groups and entire protein complexes.
Contact: eran@cs.stanford.edu
Keywords: probabilistic models, protein interaction, gene expression.
*To whom correspondence should be addressed.
Genome-wide discovery of transcriptional modules from
DNA sequence and gene expression
Authors: Segal E. , Yelensky R. , Koller D. 
Published: July 2003

Abstract
In this paper, we describe an approach for understanding transcriptional regulation from both gene expression and promoter sequence data. We aim to identify transcriptional modules—sets of genes that are co-regulated in a set of experiments, through a common motif profile. Using the EM algorithm, our approach refines both the module assignment and the motif profile so as to best explain the expression data as a function of transcriptional motifs. It also dynamically adds and deletes motifs, as required to provide a genome-wide explanation of the expression data. We evaluate the method on two Saccharomyces cerevisiae gene expression data sets, showing that our approach is better than a standard one at recovering known motifs and at generating biologically coherent modules. We also combine our results with binding localization data to obtain regulatory relationships with known transcription factors, and show that many of the inferred relationships have support in the literature.
Contact: eran@cs.stanford.edu
Keywords: probabilistic models, gene expression, transcriptional regulation.
*To whom correspondence should be addressed.
CREME: a framework for identifying cis-regulatory modules
in human-mouse conserved segments
Authors: Sharan Roded , Ovcharenko Ivan , Ben-Hur Asa , Karp Richard M. 
Published: July 2003

Abstract
Motivation: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of binding sites for transcription factors that cooperate in the regulation of genes. In this work we establish a framework for finding recurrent cis-regulatory modules in the promoters of a selected set of genes and scoring their statistical significance.
Results: Proceeding from a database of identified binding site motifs and their genomic locations we seek motifs whose frequency in the selected promoters is different than in a background promoter set. We present several statistical tests designed for this purpose. We provide a hashing algorithm for detecting combinations of these motifs that co-occur in clusters within the selected promoters. The significance of such co-occurrences is evaluated using novel statistical scores. Our methods are combined in CREME, a suite of software which includes a browser for viewing the pattern of occurrence of selected cis-regulatory modules. We applied our methodology to find modules within human-mouse conserved promoter segments, focusing on cell cycle regulated genes and stress response related genes. To validate the biological significance of the identified modules we tested whether the associated genes tended to be co-expressed or share similar function. In the cell cycle set five of the seven identified sets of genes were coherently expressed. On the stress response data four of the six detected sets fell predominantly into well-defined functional sub-categories.
Availability: http://icsi.berkeley.edu/~roded/creme.html
Contact: roded@icsi.berkeley.edu.
Keywords: Cis-regulatory module, transcription factor binding site, motif cluster, statistical test.
*To whom correspondence should be addressed.
†These authors contributed equally to this work.
A probabilistic method to detect regulatory modules
Authors: Sinha Saurabh , van Nimwegen Erik , Siggia Eric D. 
Published: July 2003

Abstract
Motivation: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity.
Results: We develop a computational method that uses Hidden Markov Models and an Expectation Maximization algorithm to detect such modules, given the weight matrices of a set of transcription factors known to work together. Two novel features of our probabilistic model are: (i) correlations between binding sites, known to be required for module activity, are exploited, and (ii) phylogenetic comparisons among sequences from multiple species are made to highlight a regulatory module. The novel features are shown to improve detection of modules, in experiments on synthetic as well as biological data.
Availability: The source code for the programs is available upon request from the authors.
Contact: {saurabh,erik,siggia}@lonnrot.rockefeller.edu
Keywords: hidden Markov model, cis-regulatory modules, motif correlations, phylogenetic comparison
*To whom correspondence should be addressed.
myGrid: personalised
bioinformatics on the information grid
Authors: Stevens Robert D. , Robinson Alan J. , Goble Carole A. 
Published: July 2003

Abstract
Motivation: The myGrid project aims to exploit Grid technology, with an emphasis on the Information Grid, and provide middleware layers that make it appropriate for the needs of bioinformatics. myGrid is building high level services for data and application integration such as resource discovery, workflow enactment and distributed query processing. Additional services are provided to support the scientific method and best practice found at the bench but often neglected at the workstation, notably provenance management, change notification and personalisation.
Results: We give an overview of these services and their metadata. In particular, semantically rich metadata expressed using ontologies necessary to discover, select and compose services into dynamic workflows.
Availability: Software is available on request from the authors and information from http://www.mygrid.org.uk
Contact: carole@cs.man.ac.uk
*To whom correspondence should be addressed.
Scaling up accurate phylogenetic reconstruction from gene-order data
Authors: Tang Jijun , Moret Bernard M.E. 
Published: July 2003

Abstract
Motivation: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods (such as neighbor-joining), parsimony methods using sequence-based encodings, Bayesian approaches, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach, but cannot handle more than about 15 genomes of limited size (e.g. organelles).
Results: We report here on our successful efforts to scale up direct optimization through a two-step approach: the first step decomposes the dataset into smaller pieces and runs the direct optimization (GRAPPA) on the smaller pieces, while the second step builds a tree from the results obtained on the smaller pieces. We used the sophisticated disk-covering method (DCM) pioneered by Warnow and her group, suitably modified to take into account the computational limitations of GRAPPA. We find that DCM-GRAPPA scales gracefully to at least 1000 genomes of a few hundred genes each and retains surprisingly high accuracy throughout the range: in our experiments, the topological error rate rarely exceeded a few percent. Thus, reconstruction based on gene-order data can now be accomplished with high accuracy on datasets of significant size.
Availability: All of our software is available in source form under GPL at http://www.compbio.unm.edu
Contact: moret@cs.unm.edu
*To whom correspondence should be addressed.
Skew in CG content near the transcription start site in
Arabidopsis thaliana
Authors: Tatarinova Tatiana , Brover Vyacheslav , Troukhan Maxim , Alexandrov Nickolai 
Published: July 2003

Abstract
We have discovered a novel statistical feature of Arabidopsis thaliana genome that remarkably correlates with a position of transcription start site—CG skew peak. We hypothesize that the phenomenon can be explained by the higher mutability of unprotected cytosines.
Keywords: CG skew, promoter, transcription, mutation, full-length cDNA
Contact: nicka@ceres-inc.com
*To whom correspondence should be addressed.
Extraction of correlated gene clusters from multiple genomic data
by generalized kernel canonical correlation analysis
Authors: Yamanishi Y. , Vert J.-P. , Nakaya A. , Kanehisa M. 
Published: July 2003

Abstract
Motivation: A major issue in computational biology is the reconstruction of pathways from several genomic datasets, such as expression data, protein interaction data and phylogenetic profiles. As a first step toward this goal, it is important to investigate the amount of correlation which exists between these data.
Results: These methods are successfully tested on their ability to recognize operons in the Escherichia coli genome, from the comparison of three datasets corresponding to functional relationships between genes in metabolic pathways, geometrical relationships along the chromosome, and co-expression relationships as observed by gene expression data.
Contact: yoshi@kuicr.kyoto-u.ac.jp
*To whom correspondence should be addressed.
Evaluation of text data mining for database curation:
lessons learned from the KDD Challenge Cup
Authors: Yeh Alexander S. , Hirschman Lynette , Morgan Alexander A. 
Published: July 2003

Abstract
Motivation: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process. To date, the lack of standards has made it impossible to determine whether text mining techniques are sufficiently mature to be useful.
Results: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup. We provided a training corpus of 862 articles consisting of journal articles curated in FlyBase, along with the associated lists of genes and gene products, as well as the relevant data fields from FlyBase. For the test, we provided a corpus of 213 new (‘blind’) articles; the 18 participating groups provided systems that flagged articles for curation, based on whether the article contained experimental evidence for gene expression products. We report on the evaluation results and describe the techniques used by the top performing groups.
Contact: asy@mitre.org
Keywords: text mining, evaluation, curation, genomics, data management
*To whom correspondence should be addressed.
Extracting synonymous gene and protein terms from biological literature
Authors: Yu Hong , Agichtein Eugene 
Published: July 2003

Abstract
Motivation: Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance.
Results: We have explored four complementary approaches for extracting gene and protein synonyms from text, namely the unsupervised, partially supervised, and supervised machine-learning techniques, as well as the manual knowledge-based approach. We report results of a large scale evaluation of these alternatives over an archive of biological journal articles. Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database.
Data Availability: The extracted gene and protein synonyms are available at http://synonyms.cs.columbia.edu/
Contact: {hongyu,eugene}@cs.columbia.edu
*To whom correspondence should be addressed.
Do Committees Ru(i)n the Bio‐Political Culture? On the Democratic Legitimacy of Bioethics Committees
Authors: Friele Minou Bernadette 
Published: July 2003

AbstractBioethical and bio‐political questions are increasingly tackled by committees, councils, and other advisory boards that work on different and often interrelated levels. Research ethics committees work on an institutional or clinical level; local advisory boards deal with biomedical topics on the level of particular political regions; national and international political advisory boards try to answer questions about morally problematic political decisions in medical research and practice. In accordance with the increasing number and importance of committees, the quality of their work and their functional status are being subjected to more and more scrutiny. Besides overall criticism regarding the quality of their work, particular committees giving political advice are often suspected of being incompatible with democratic values, such as respect for affected parties, representation of diverse values and transparency in the decision‐making processes. Based on the example of the German National Ethics Council, whose inauguration caused a still ongoing debate on the aims and scopes of committees in general, this paper discusses: (1) the requirements of modern democratic societies in dealing with complex scientific‐technical problems; (2) the composition and organisation of committees working as political advisory boards; and (3) the appointment procedures and roles of laymen and experts, and here in particular of ethicists, who may legitimately be taken on by a committee.I will argue that bioethics committees do not necessarily endanger democratic values, but can considerably improve their realisation in democratic decision‐making procedures – if, and only if, they do not act as substitutes for parliamentarian processes, but help prepare parliamentarian processes to be organised as rationally as possible.
Should Consensus Be ‘The Commission Method’ in the US? The Perspective of the Federal Advisory Committee Act, Regulations, and Case Law
Authors: Spielman Bethany 
Published: July 2003

AbstractThis paper examines the drive for consensus from the perspective of the good government framework for federal advisory commissions in the United States. Specifically, the paper examines the Federal Advisory Committee Act (FACA) – the statute, its regulations, and case law. It shows that the FACA was intended to be an antidote to abuses in consensus‐making processes, including the failure to fully include competing views on commissions. The index of suspicion in the FACA scheme rises when a group work product – including a consensus report – is to be the basis of recommendations to federal officials. Once FACA's requirements regarding committee composition are satisfied, the index of suspicion drops and FACA is indifferent to consensus‐making; but the conditions for informed, meaningful participation apply to members who dissent from, as well as those who participate in, consensus. In negotiated rulemaking, the push for consensus and closure creates unacceptable tension with the good government goals of openness and accountability. Proponents of consensus‐only bioethics commissions can learn from FACA‐related legislative, agency, and judicial insights that consensus‐seeking is not always desired by government officials; is rarely cost free; and that diversity and dissent enhance openness, accountability, and fairness. The burden of proof is therefore on proponents of a consensus‐only standard for bioethics commissions to demonstrate that a drive for consensus furthers sound decision‐making by government officials more than it sets back openness and accountability to a diverse public.
The Role of National Ethics Commissions in Finland
Authors: Halila Ritva 
Published: July 2003

AbstractThere are six national ethics commissions in Finland. The National Advisory Board on Research Ethics was first established in 1991, followed by the National Advisory Board on Biotechnology and the Board on Gene Technology in 1995. The National Advisory Board on Health Care Ethics was established in 1998, followed by its Sub‐Committee on Medical Research Ethics in 1999. The Co‐operation Group for Laboratory Animal Sciences was established in 2001. Only the Board on Gene Technology works as a national authority and gives binding opinions and recommendations about the use of genetically modified organisms. The Sub‐Committee on Medical Research Ethics acts as a national research ethics committee and gives opinions about research projects. Other advisory boards do not make legally binding decisions, but their expertise gives a lot of power to their opinions and statements.The commissions work in close collaboration with each other, having regular meetings. They arrange seminars and conferences, and share information with each other. The commissions also share duties and information in international collaboration.How the voice and opinions of these commissions is heard in society lies in the wide, multi‐professional expertise of their members. Large commissions and wide expertise may make it difficult to find consensus in their opinions and statements, although wide expertise may, more than discussion in a small expert group, help to further process difficult ethical issues.Collaboration between different bodies is important in order to share duties, and also to add more emphasis to the statements and opinions where different bodies share interests. In our country, the interest that national commissions share is research ethics, where the advisory boards and their members have discharged collaborative activities for years.
Testing of Fractional Cointegration in Macroeconomic Time Series*
Authors: Gil‐Alana Luis A. 
Published: July 2003

AbstractWe propose in this article a two‐step testing procedure of fractional cointegration in macroeconomic time series. It is based on Robinson's (Journal of the American Statistical Association, Vol. 89, p. 1420) univariate tests and is similar in spirit to the one proposed by Engle & Granger (Econometrica, Vol. 55, p. 251), testing initially the order of integration of the individual series and then, testing the degree of integration of the residuals from the cointegrating relationship. Finite‐sample critical values of the new tests are computed and Monte Carlo experiments are conducted to examine the size and the power properties of the tests in finite samples. An empirical application, using the same datasets as in Engle & Granger (Econometrica, Vol. 55, p. 251) and Campbell & Shiller (Journal of Political Economy, Vol. 95, p. 1062), is also carried out at the end of the article.