What PubAtlas Does
PubAtlas is a program that acts as a front-end to PubMed.
As input it takes two sets of "terms",
which are text lines having one of the two formats
and analyze them in a table of associations.
concept phrase : PubMed Query
For example, we could find associations between people and genes.
Our first set of terms should then be queries about people:
Pound signs (#) and everything after them are ignored, permitting comments about the queries.
# Project Direction
Bob Bilder: Bilder Robert [FAU] OR Bilder R [AU] # Director of CNP
Roberto Peccei: Peccei Roberto [FAU] OR Peccei R [AU]
Leonard Rome: Rome Leonard [FAU] OR Rome LH [AU]
Fred Sabb: Sabb Fred [FAU] OR Sabb FW [AU]
# Cognitive Neuroscience
Carrie Bearden: Bearden Carrie [FAU] OR Bearden CE [AU]
Bob Bilder: Bilder Robert [FAU] OR Bilder R [AU]
Ty Cannon: Cannon Tyrone [FAU] OR Cannon TD [AU]
PubMed permits use of many
search field 'tags' like '[AU]' indicating that the text preceding the tag
is to be interpreted as a specific kind of information, and used as a search key in the corresponding PubMed index.
In this example, the [AU] Author name tag
indicates that the preceding text is a name (a last name followed by initials).
The [FAU] Full Author name tag
is used whenever full names are used instead of initials.
The second set of terms should be queries about gene identifiers, like these:
PubAtlas takes these two sets of terms and evaluates all PubMed associations
between the first set (people) and the second (genes),
and yields a table like the following:
DAT1: "DAT1" [TIAB] OR "DAT-1" [TIAB]
DRD2: "DRD2" [TIAB] OR "DRD-2" [TIAB] OR ("D2" [TIAB] AND "dopamine receptor" [TIAB])
DRD4: "DRD4" [TIAB] OR "DRD-4" [TIAB] OR ("D4" [TIAB] AND "dopamine receptor" [TIAB])
DRD5: "DRD5" [TIAB] OR ("D5" [TIAB] AND "dopamine receptor" [TIAB])
SNAP2: "SNAP2" [TIAB] OR "SNAP-25" [TIAB]
PubAtlas also has a number of
predefined term sets
— vocabularies of typically about 100 terms
that can be used as "shotgun" association finders.
The table above can be generated easily by just using the predefined sets for CNP people and CNP genes,
with an input screen like this:
For more information see the
The PubAtlas Gallery
also has examples that show what PubAtlas can do.
Familiarity with PubMed can help you succeed with PubAtlas.
There is an extensive
online tutorial/reference/help system for PubMed.
page has links to information about important PubMed features.
This knowledge is important; being aware of how PubMed interprets queries enables you to
find associations (and relevant publications) that otherwise might be missed.
Spending 10 minutes looking through this may end up saving you hours of search.
the Medical Subject Heading "ontology" used by PubMed, is also important.
MeSH is a kind of keyword index, or set of indexing terms or topics.
As articles are entered into PubMed they are tagged by curators as
being relevant to certain MeSH terms, so that we can search articles by topic.
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