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Acumenta Corporation provides three products:
Acumenta Literature Lab™
"Information overload" in the scientific literature is more than an abstract concept or a wry remark; it is a
serious problem facing research scientists in biotechs, pharmaceutical companies and academia. The number
of scientific journal abstracts on PubMed that reference one or more human genes has exceeded 2.5 million. About
65,000 new abstracts are currently being added to PubMed every month and this number
is steadily increasing. One third of these abstracts mention one or more human genes.
In the face of this wealth of scientific reporting, conventional literature review as practiced by most
research scientists is an anachronism. There is too much literature to find, assimilate and keep pace with
using conventional manual searching. Furthermore, conventional searching is unlikely to identify novel
connections and subtle relationships that are subsequently useful in the laboratory.
Literature Lab™ is a powerful text analytics/text mining solution created by Acumenta specifically to solve these
problems for researchers in the life sciences and to help them accelerate their research. It enables scientists
to accelerate identification of testable hypotheses through accurate enrichment of any list of genes or proteins in
pathways, diseases compounds/drugs and other dimensions, with relationships that the scientist can explore in the
literature with a single mouse click.
Through rigorous analysis of the most recent 10 million PubMed abstracts (1990 to the present), important and
unanticipated lines of inquiry are revealed by Literature Lab on a single Highlights page. Literature Lab™
eliminates conventional PubMed searching while assuring the scientist that every PubMed abstract has been
reviewed for content that enriches his or her gene list.
A Literature Lab™ analysis on 50 genes is the equivalent of 3.8 Billion manual searches.
NLP-based approaches and summarization engines provide useful reading material to the scientist.
However Literature Lab™ is advancement because it enriches scientists’ genes of interest in multiple
biological domains, identifying research inflection points and accelerating the track to new learning and
meaningful testable hypotheses. Some important differences include:
- Literature Lab™ bases its analysis on the similarities within a group of genes
- Literature Lab™ performs numerical and statistical analysis on co-occurrences
that exist in the literature to identify novel areas of exploration
- Literature Lab™ provides comparisons among multiple enriched data sets
In the case of analysis of microarray experiment data Literature Lab™ differs greatly from and is
complimentary to curated databases and ontology-based approaches to understanding results of experiments.
It has the advantage of connecting the scientist directly to the literature that describes the biological
functions significantly associated with their work. Insights and annotations can be added to Literature Lab™
results and made sharable with colleagues, accelerating organizational learning and response to new ideas.
View a video introduction to Literature Lab™.
Read an article in BMC Genomics about Literature Lab™ and its application.
Request more information
The Acumenta Gene Thesaurus™
The Acumenta Gene Thesaurus is a complete repository of human gene and protein nomenclature. It contains symbols,
names and aliases gathered from every major biomedical repository combined with extensive human and machine curation
to assure comprehensive and precise searching of literature on gene and protein topics. Ask us how to incorporate
this valuable taxonomy into your search applications.
Please contact Acumenta for further information.
The Acumenta Online Research Assistant™
The Online Research Assistant is for scientists and information professionals in the life sciences.
Running on a researcher's desktop or laptop computer, Acumenta software enables researchers to create queries
that yield substantially superior results when compared to direct searching of PubMed, patents and other
biomedical databases.
Benefits of the Online Research Assistant
Use of Acumenta typically saves between 50% and 70% of scientists' online
research time and, more importantly, enables R&D scientists to:
- Locate and use critical research findings that may impact R&D
project outcomes.
- Perform literature-based hypothesis generation and refinement.
- Find important information treasures, such as key science hidden
in patent documents and other biomedical databases, that would otherwise
not be found.
- Keep current with the latest scientific developments.
- Capture thinking in the context of specific external research documents
and, where appropriate, share these insights with a project team and
other colleagues in the R&D organization.
The Acumenta Online Research Assistant™ in More Detail
The Online Research Assistant represents a new, easier way to accomplish the important
tasks of online research and literature review. To integrate smoothly
into the workflow of the research scientist, the Online Research Assistant supports
all three types of online research queries:
- One-time, interactive questions, often to test hypotheses,
plan lab experiments or verify results
- Retrospective research questions where it is important
to save the results for incorporation into a presentation, report or
publication
- Ongoing current awareness queries where staying
up-to-date is critical.
To ensure that high quality search results are retrieved, a rapid, interactive,
search tuning process for all three types of queries is provided by the
software.
The Online Research Assistant was designed by working directly with life scientists
to understand the problems inherent in conducting online research the
traditional way. These online research hurdles are addressed in some very
unique ways by the Acumenta software and Acumenta Gene Thesaurus™.
Answers to the following questions should provide some understanding of
how Acumenta Online Research Assistant™ operates.
What is different about the Acumenta searching process versus searching
PubMed, USPTO and other databases directly? The Online Research Assistant:
- Supports easy formulation, testing and tuning of
powerful queries prior to execution and maintains a query database.
- Searches multiple databases simultaneously with
a single query.
- Runs searches on full experimental gene sets (including
other search words) in a single query.
- Executes literature and patent queries and downloads results
automatically to a researcher's desktop or laptop.
- Provides the Acumenta Gene Thesaurus™ for
increased relevancy (precision) and thoroughness (recall) of search
results.
How does the Online Research Assistant facilitate the process of literature and patent document
review, assimilation and information management? The Online Research Assistant:
- Inserts navigation links into patent and other lengthy
documents for quick access to important sections and search terms.
- Highlights search terms as well as terms of importance
for faster, more thorough review.
- Provides Retain/Discard buttons to enable the scientist
to keep valuable literature and eliminate irrelevant documents.
- Does not retrieve the same discarded documents again
in the case of ongoing queries.
- Exports results to Microsoft Excel®, EndNote®
and Reference Manager®.
How does Acumenta help life scientists extract new meaning and biological
relationships from search results? Acumenta Online Research Assistant™:
- Prepares a gene co-occurrence analysis in the case
of experimental gene set queries.
- Identifies experts and their standing in a scientific
field using Acumenta's Author Analysis.
How does the Online Research Assistant enable a life scientist to stay on top of important
developments relevant to his or her field? Acumenta software:
- Automates "what's new" for ongoing
current awareness by delivering and organizing this information for
presentation in the browser.
How does Acumenta extend, augment and preserve valuable search results
and the individual thinking of R&D scientists? The Online Research Assistant:
- Maintains and updates individual scientist knowledgebases
of literature, patent documents and other biomedical information.
- Enables the capture of both private and public researcher
annotations at the document level.
- Enables the sharing of search results and annotations
with colleagues and collaborators.
- Delivers all public annotations associated with an external
research document when it is retrieved by subsequent queries
by any scientist within the R&D organization.
The net result: the Online Research Assistant increases the level of preparedness of individual
scientists, R&D project teams and the entire R&D organization.
No incremental IT infrastructure is required for the Online Research Assistant
software or the shared annotation and search results capability.
There are many more capabilities in the Acumenta software. Contact us
to see a demonstration and to arrange an
Acumenta trial. |
