The Reach information extraction system reads biomedical publications and identifies a sequence of biochemical events that involve interactions among, or modifications of, physical entities; such as proteins, genes, small molecules, metabolites, and so on. In 2015, the Reach Results Explorer extracted 2.685 million interaction events (and their participant entities) from a corpus of over 175,000 cancer-related PubMed publications. The Results Explorer allows interactive exploration of that result space using a simple agent-predicate-patient matching paradigm.
Events may be queried by any combination of
agent entity,
event interaction type (aka predicate),
patient entity, and/or
PubMed Central document ID.
Four color-coded boxes allow the entry of the corresponding query
terms. After entering query terms, press the
Explore
button to search the Reach results
for events matching the specified combination of entities and
interaction.
Click on a (view) link, next to a
PubMed Central document ID,
to view the paper online at PubMed Central.
For event-oriented exploration of the Reach results, begin by
selecting an interaction type from the
Predicate drop down box and
press the Explore
button. To further
restrict the event participants, enter entity names in the
Agent and/or
Patient search boxes,
and/or a PMC ID in the Document search
box, as appropriate for your inquiry.
For entity-oriented exploration of the Reach results, begin by
entering an entity of interest in the
Agent and/or
Patient search boxes.
Then, press the Explore
button
to see what relationships the entered entity (or entities) participate
in. To restrict the results to a specific type of interaction, select
an interaction type from the
Predicate drop down box, as appropriate
for your inquiry.
The total number of events matching the current query is shown in red at the right side of the Agent-Predicate-Patient-Document Search panel.
Four color-coded panels display the results for all events matching a given query. The Top Agents, Top Patients, and Top Documents panels show the 40 most frequently occurring participants in the matching events, in descending order of frequency. Clicking on a participant in one of the Top Agents, Top Patients, or Top Documents panels quickly enters or removes the participant from the corresponding search box, in preparation for another exploration or fetch.
The Predicates panel shows the interaction type categorizations and totals for all events matched by the current query. Note that since the interaction type categories are not mutually exclusive, events are often counted in more than one category.
Reach search results may also be displayed in the context of a
single sentence by using the
Fetch
button.
To view the complete paper online at PubMed Central,
click on a (view) link next to a
PubMed Central document ID.
The number of results displayed in sentential context is controlled by
using the "fetch limit" drop down box (directly to the left of the
Fetch
button). (Note that the number of
results displayed will never exceed the number specified in the "fetch
limit" drop down box, even if there are more results that could be
displayed).
Search results may be re-fetched and sorted in a different order
by using the
Sort By
and
Sort Direction
buttons.
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