XplorMed glossary
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XplorMed glossary

Abstract
The summary of a paper.

Alpha
All the relations from a word to another have an associated strength value. Alpha is a threshold to be applied on the relationships to be used for computing word chains. If you raise it, you will get less connections. If you lower it, you will get more connections.

Databases
An entry from a database with links to MEDLINE can be used as input to XPlorMed. We will read the links to MEDLINE from the entry, and retrieve the corresponding abstracts from PubMed. Currently, the following databases are implemented: SwissProt, SPTrembl, OMIM, SMART, and of course MEDLINE.

Input formats
The input format can be either medline, endnote, xml, or xplormed.
  • Abstracts in medline format can be obtained through the NCBI's PubMed server. After searching, select the MEDLINE format in the display menu after the Display button, and hit the Save button. See an example.
  • Abstracts in endnote format can be obtained through the BioMedNet server. After searching, select the Endnote format in the display menu below the search results. Tick the "Download Refs" ratio button and hit the "Get All" button. See an example.
  • Abstracts in xml format can be obtained through the NCBI's PubMed server. After searching, select the XML format in the display menu after the Display button, and hit the Save button. See an example.
  • Abstracts in xplormed format can be obtained from selections of your input via XplorMed. This is the internal format into which we convert any input. The format consists on one line per abstract with fields separated by tabs corresponding to: pubmed id, title, abstract, date, journal, MeSH terms, medline id, publication type, authors. See an example.

Lemma
It is the group of all inflected forms of a word. For example, the lemma of all the forms of a verb is the infinitive (e.g., "be" for "is", "were", or "was"). The lemma of a plural is the singular (e.g., "foot" for "feet", or "protein" for "proteins").

MEDLINE neighbours
Abstracts with a similar word content to a given one. Two neighbouring abstracts would be expected to deal with similar subjects. (To known more).

MeSH terms
Each MEDLINE entry is indexed with a set of terms (MeSH terms compiled at the NLM) grouped in eight main categories. MeSH stands for Medical Subject Headings. If you want to know more, visit the MeSH page at the National Library of Medicine.

Score
Each word has a score that indicates how much the word is associated to others. Score is a threshold to be applied to the words to be used for computing the word chains. If you raise it, then you will compute relationships on less words, and therefore you will obtain less relationships. Lower it, if you want to include more terms.

Word
In this version of XplorMed, the words considered are the lemmas (e.g., the singular form) of nouns. Take this into account if you are asked to provide a word. For example, "gene" will be valid, but not "genes".

Word chain
An ordered set of words where the 2nd depend on the 1st, the 3rd depends on the 2nd, an so on.

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