2,474 research outputs found
Comparative Analyses of Plant Transcription Factor Databases
Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed
Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at http://www.esat.kuleuven.be/abandapart/
Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article
Scientific innovation depends on finding, integrating, and re-using the products of
previous research. Here we explore how recent developments in Web technology,
particularly those related to the publication of data and metadata, might assist that
process by providing semantic enhancements to journal articles within the mainstream
process of scholarly journal publishing. We exemplify this by describing semantic
enhancements we have made to a recent biomedical research article taken from
PLoS Neglected Tropical Diseases, providing enrichment to its
content and increased access to datasets within it. These semantic enhancements
include provision of live DOIs and hyperlinks; semantic markup of textual terms, with
links to relevant third-party information resources; interactive figures; a
re-orderable reference list; a document summary containing a study summary, a tag
cloud, and a citation analysis; and two novel types of semantic enrichment: the
first, a Supporting Claims Tooltip to permit “Citations in
Context”, and the second, Tag Trees that bring together semantically
related terms. In addition, we have published downloadable spreadsheets containing
data from within tables and figures, have enriched these with provenance information,
and have demonstrated various types of data fusion (mashups) with results from other
research articles and with Google Maps. We have also published machine-readable RDF
metadata both about the article and about the references it cites, for which we
developed a Citation Typing Ontology, CiTO (http://purl.org/net/cito/). The
enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, presents a
compelling existence proof of the possibilities of semantic publication. We hope the
showcase of examples and ideas it contains, described in this paper, will excite the
imaginations of researchers and publishers, stimulating them to explore the
possibilities of semantic publishing for their own research articles, and thereby
break down present barriers to the discovery and re-use of information within
traditional modes of scholarly communication
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
The last twenty years have witnessed molecular data emerge as a primary
research instrument in most branches of mycology. Fungal systematics, taxonomy,
and ecology have all seen tremendous progress and have undergone rapid,
far-reaching changes as disciplines in the wake of continual improvement in DNA
sequencing technology. A taxonomic study that draws from molecular data
involves a long series of steps, ranging from taxon sampling through the
various laboratory procedures and data analysis to the publication process. All
steps are important and influence the results and the way they are perceived by
the scientific community. The present paper provides a reflective overview of
all major steps in such a project with the purpose to assist research students
about to begin their first study using DNA-based methods. We also take the
opportunity to discuss the role of taxonomy in biology and the life sciences in
general in the light of molecular data. While the best way to learn molecular
methods is to work side by side with someone experienced, we hope that the
present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology -
comments most welcom
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