Wednesday, February 22, 2012

  1. Name at least three searchable types (categories) of information that are contained in
MEDLINE abstracts

Title, author, journal issue, text words.

  1. What are MeSH terms and what is their purpose?

MeSH (Medical Subject Headings) is controlled vocabulary thesaurus used for
indexing articles in MEDLINE/PubMed. MeSH terms are organized in hierarchical
structure that allows searching at various levels of specificity. They follow hierarchy format and NOT DAG so NOT ontologies.

Q34: How can a search result be “expanded” (I refer to the PubMed help, where “expansion of search results” is a separate point)
Answer: If this question means to expand the search result if I have retrieved too few citations, then here are the following steps you need to do.
·       Click the Related citations See all link for a relevant citation to display a pre-calculated set of PubMed citations closely related to the article.
·     Remove extraneous or specific terms from the search box.
·     Try using alternative terms to describe the concepts you are searching.

  1. Explain “information retrieval” with an example involving Medline and MeSH terms
MEDLINE uses Medical Subject Headings (MeSH) for information retrieval. Engines designed to search MEDLINE (such as Entrez and PubMed) generally use a Boolean expression combining MeSH terms, words in abstract and title of the article, author names, date of publication, etc. Entrez and PubMed can also find articles similar to a given one based on a mathematical scoring system that takes into account the similarity of word content of the abstracts and titles of two articles.

  1. When do we speak of synonyms and when do we speak of homonyms?

Synonyms are different words with identical meaning.
Homonyms are identical words with different meaning.

  1. Sketch the major concepts and the conceptual schema of MedLine
Journal, Author Name, Article,Publication date, References

  1. Explain the differences between OMIM and MedLine
Both OMIM and Medline are literature-based databases. However the OMIM database
is a catalog of human genes and genetic disorders. An entry in OMIM is a review
focusing on a disease, its phenotypic appearance and the genes involved in the
molecular etiology of the disease. Whereas Medline is a bibliographic database
covering a broad scope of biosciences.

OMIM is a bibliographic database which contains information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.
Bibliographic database that cites abstracts from Biomedical journals
A database which provides access to curated data gathered from public scientific literature as well as other sources
Medline, a database of indexed abstracts from scientific biomedical literature
Each entry is obtained and compiled from several reference sources.
Each entry corresponds to a single journal article.
OMIM does not employ MeSH terms
Uses controlled vocabulary called as MeSH (Medical subject headings)
OMIM is a heavily curated database
MEDLINE is  also a curated database.
OMIM is focused on human disease and gathers any kind of information which helps to understand the cause of disease.
Medline contains details of mutagenesis experiments whose relevance might be yet to be established.

  1. What are the three root concepts of GO?

Molecular function : the elemental activities of a gene product at the molecular level, such as  binding or catalysis
Biological processes: operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissuesorgans, and organisms.
Cellular Component: the parts of a cell or its extracellular environment.
  1. What means “annotation”?

A combination of comments, notations, references, and citations, either in free format
or utilising a controlled vocabulary, that together describe all the experimental and
inferred information about a gene or protein. Annotations can also be applied to the
description of other biological systems. Batch, automated annotation of bulk biological
sequence is one of the key uses of Bioinformatics tools.

  1. Which controlled vocabularies do you know besides GO?

MeSH, HGNC, sequence Ontology, Brenda enzyme source ontology, EMAP,
SwissProt keywords, MAGE-OM
·         GO
·         MeSH (Medical subject Headings)
·         IUPAC
·         EC (Enzyme nomenclature)

  1. Name three of the most important / most informative entity-types that can be found in
EMBL or EntrezGene

Entity-types: organism, molecule, sequence.

  1. Which objects in biology correspond to these entity-types?
Organism: animals, plants, fungi, bacteria, protozoa.
Molecule: DNA, RNA.
Sequence: nucleic acid sequence, i.e. adenine, thymine, guanine, cytosine in case of
DNA; adenine, uracil, guanine, cytosine in case of RNA.

  1. Define a gene and name three attributes
A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence region.
Gene is a unit of DNA which performs one function. Usually, this is equated with the production of one RNA or one protein. A gene contains coding regions, introns, untranslated regions and control regions.
Intron & exon positions
Protein binding sites

  1. Who is the owner of an entry in EMBL?
The person who submits (submitter) the gene sequence (or any entry) to the EMBL database is the owner. The authority to change that entry is also with the submitter.

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