GeneNarrator: Mining the Literaturome
for Relations Among Genes
, Daniel Berleant2*
, Jun Xu3
, Eve Wurtele5
, Andy Fulmer6
Information Warehouse, Ohio State University Medical Center, 410 W.
Columbus, Ohio, 43210, USA, firstname.lastname@example.org, (614) 293-0776, fax (614) 293-2210
Department of Information Science, University of Arkansas at Little Rock,
2801 University Ave.,
Little Rock, Arkansas, 72204, USA, email@example.com, (501) 683-7056, fax (501) 683-7049
Miami Valley Laboratories, The Procter and Gamble Company,
11810 East Miami River Rd., Ross, Ohio, 45061, USA, firstname.lastname@example.org
Miami Valley Laboratories, The Procter and Gamble Company,
11810 East Miami River Rd., Ross, Ohio, 45061, USA, email@example.com
Department of Genetics, Development and Cell Biology,
Iowa State University, Ames, Iowa, 50011, USA, firstname.lastname@example.org
Miami Valley Laboratories, The Procter and Gamble Company,
11810 East Miami River Rd., Ross, Ohio, 45061, USA, email@example.com
||Dr. Daniel Berleant, Department of Information Science,
University of Arkansas at Little Rock,
2801 University Ave., Little Rock,
Arkansas, 72204, USA,
Tel : (501) 683-7056,
Fax : (501) 683-7049,
E-mail : firstname.lastname@example.org
|Received July 07, 2009; Accepted August 23, 2009; Published August 24, 2009
Citation: Ding J, Berleant D, Xu J, Juhlin K, et al. (2009) GeneNarrator: Mining the Literaturome for Relations
Among Genes. J Proteomics Bioinform 2: 360-371. doi:10.4172/jpb.1000096
Copyright: © 2009 Ding J, et al. This is an open-access article distributed under the terms of the Creative Commons
Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author
and source are credited.
The rapid development of microarray and other genomic technologies now enables biologists to monitor the
expression of hundreds, even thousands of genes in a single experiment. Interpreting the biological meaning of the
expression patterns still relies largely on biologists domain knowledge, as well as on information collected from
the literature and various public databases. Yet individual experts’ domain knowledge is insufficient for large data
sets, and collecting and analyzing this information manually from the literature and/or public databases is tedious and
time-consuming. Computer-aided functional analysis tools are therefore highly desirable.
We describe the architecture of GeneNarrator, a text mining system for functional analysis of microarray data.
This system’s primary purpose is to test the feasibility of a more general system architecture based on a two-stage
clustering strategy that is explained in detail. Given a list of genes, GeneNarrator collects abstracts about them
from PubMed, then clusters the abstracts into functional topics in a first clustering stage. In the second clustering
stage, the genes are clustered into groups based on similarities in their distributions of occurrence across topics.
This novel two-stage architecture, the primary contribution of this project, has benefits not easily provided by onestage
|Genes; Clustering; Text mining
|Rapid developments in genomic technologies such as
microarrays now enable biologists to simultaneously
monitor the expression of thousands of genes in a single
experiment. Automated data analysis methods and software
tools are important for efficiently processing the resulting
large amounts of data. Numerous algorithms and
tools have been developed for finding patterns in gene
expression and grouping genes with similar patterns.
Interpreting the biological meanings of the patterns,
however, still largely relies on human experts’ domain
knowledge, as well as on manual collection of previously
reported results. Human expertise works well when experts
are available, as for specific domains and their relatively
modestly sized data sets. However, human expertise
can be expensive. It is also not always available. For
example systems biology research often depends on interdisciplinary
collaborations across multiple domains.
That is in the nature of large, complex systems. Some of
the researchers might not be experts in even one domain,
students are often involved who are not domain experts,
and in any case it is unrealistic to expect even domain
experts to memorize functional details of thousands of
genes. The alternative of manually collecting and analyzing
them from the literature and public databases is tedious
and time-consuming. Therefore, computer-aided
functional analysis tools are a critical need. To help meet
this need, this work contributes a novel two-stage clustering
architecture for which, using a test implementation
called GeneNarrator, we demonstrate the feasibility.
Related Work and Motivation
|Numerous system architectures for functional analysis
of microarray data, and the systems that demonstrate them,
have been reported in the literature. In terms of the sources
of the functional information they rely on, they can be
grouped into two categories.
||Architectures that rely on curated lexicons, ontologies,
and other such functional annotation sources, such as
the Gene Ontology (Adryan and Schuh, 2004; Badea, 2003; Joslyn et al., 2004; Kennedy et al., 2004; Pasquier et al., 2004; Robinson et al., 2004; Smid and Dorssers, 2004; Khatri and Draghici, 2005; Masys et al., 2001; and Kankar et al., 2002). Another well-know curated
resource is Reactome (http://www.reactome.org), and
there are others as well.
||Architectures that derive functional information from
MEDLINE and other text resources (Becker et al., 2003; Chaussabel and Sher, 2002; Homayouni et al., 2005; Kim and Falkow, 2003; Oliveros et al., 2000; Raychaudhuri and Altman, 2003; Raychaudhuri et al., 2002; Renner and Aszodi, 2000; Slaton and McGill, 1983, Glenisson et al., 2003; Chagoyen et al., 2006; Shatkay et al., 2000; and Mao et al., 2005).
These categories are further discussed next.
Using GO, a representative curated resource
|The Gene Ontology (GO) is a controlled vocabulary for
describing genes. Its development by a group of member
organizations started in 1998, and is coordinated by the
Gene Ontology Consortium. The GO Consortium also
acts as a repository of gene and gene product annotations
contributed by member organizations, e.g., FlyBase, the
Saccharomyces Genome Database (SGD) and the Mouse
Genome Database (MGD). This makes it a valuable source
of functional information for annotating microarray experiments,
and various groups have explored strategies
for using this information to functionally summarize gene
clusters. A review of ontologies for functional annotation
is provided by Khatri and Draghici, (2005).
Not all works in this category focus on GO. For example
Masys et al., (2001) and Kankar et al., (2002) used
MeSH terms, the former also using EC numbers. The
above-mentioned works shared some limitations that result
from attributes of GO and are also common in other
curated data sources.
||The GO itself, exemplifying the types of problems
common for such resources, is not static and mature.
As one consequence, its development is unbalanced.
While some branches are deep (up to 18 levels) and
contain very detailed concepts (e.g., GO:0000201 –
nuclear translocation of MAPK during cell wall biogenesis),
the GO coverage in some areas of biology is
incomplete, for example in pathways (Mao et al., 2005)
and immunology (Joslyn et al., 2004).
||The GO is updated regularly, so keeping annotations
constantly compatible with the latest GO release is a
challenge. And, even the latest release of such a resource
may not be up to date as there is a time lag
between when new data is available in the literature
and when it is annotated and placed into databases.
||GO annotations are mainly curated manually so, as
with other human-curated information sources, inconsistencies
are endemic. Thus for example Badea, (2003)
had to correct numerous mistakes in the Proteome
HumanPSD database by hand before performing the
||GO annotations are mainly available for well-studied
genes in a few model organisms. Badea, (2003) could
find annotations for only 26% (39 out of 149) of the
genes of interest. Analysis based on such incomplete
data can be risky.
Text-based functional analysis
|One approach to overcoming limitations of systems relying
on controlled ontologies is to extract functional information
from the texts in online literature databases such
as MEDLINE and its PubMed portal (http://www.ncbi.nlm.nih.gov/pubmed/). Other keyword-searchable
literature resources like CiteXplore (http://www.ebi.ac.uk/citexplore/) could also be used. Text analysis
can be deep or shallow. For example, the deep part of
the spectrum includes parsing, template matching, and
inference of causal relationships among biomolecules
based on the properties of individual sentences.
Shallow analysis can lead to sophisticated annotation
systems that facilitate navigating in the biomedical literature
by adding hyperlinks and related tools, like Whatizit
iHOP (http://www.ihop-net.org/), and WikiHyperGlossary
Shallow analysis can also lead to fine-grained retrieval of
specific parts of documents, as with MedMiner, a tool that
retrieves individual sentences from MEDLINE (Tanabe
et al., 1999). But shallow methods can also feed into deeper
analyses of text collections. Often this starts with viewing
texts as collections of words. Such methods are called
bag of words (BOW) approaches.
Texts are typically so complex and unstructured that deep
analysis can be cumbersome, especially for large quantities
of text, as well as error-prone. These problems will
likely remain until the grail of full natural language understanding
is finally reached at some unknown future
time. Interpretation errors will tend to propagate through
subsequent inferences, negatively impacting results.
Therefore it is useful for text mining system architectures
to robustly resist the effects of such text interpretation
“noise,” and shallow analysis is one strategy.
On the other hand, there are limitations to shallow analysis
methods as well. An obvious limitation is that the rich
information content in a text is not fully harvested. Another
limitation is that the reliability of one text may be
much greater than that of another, because the quality of
some publications is much greater than that of others,
and this is hard to determine automatically. The least reliable
texts tend to be less likely to be included in major corpora, which helps but does not fully address the problem.
A third limitation is that texts in different languages
are difficult to match with one another because translation
is needed first. Although potentially feasible, a translation
preprocessing step is not yet a component of most
text mining systems.
Bag-of-words based text analysis
|Text-based functional analysis systems based on the
shallow bag-of-words paradigm can be divided into two
subcategories, those that make the assumption that genes
with similar expression patterns are involved in the same
functional pathways, and those that do not. The assumption
suggests that MEDLINE abstracts referring to a gene
in a cluster of genes with similar expression patterns have
significant properties in common that provide hints about
the cluster’s functional properties. Oliveros et al., (2000)
for example focused on the words in MEDLINE abstracts.
The significance of a word to a particular cluster of similarly
expressed genes was determined by a z-test against
its average frequency in abstracts relevant to any gene
However, the assumption that similar expression patterns
necessarily mean genes are functionally related is
problematic. For example, genes involved in different
pathways may have similar expression patterns in a particular
experiment, and a single gene may participate in
several pathways. In either case, the genes in a cluster
would tend to represent different pathways, making their
interpretation more difficult. This motivates extracting
functional similarities without the assumption. That in
turn means clustering based on something other than gene
Chagoyen et al., (2006) used non-negative matrix factorization
(NMF) to process sets of abstracts related to
specific genes. The result was a vector characterizing a
given gene in terms of “semantic features,” which are
weighted, semantically relevant terms extracted automatically
from the texts. The vectors of different genes can
then be compared in order to cluster genes into “functionally
coherent” sets. A limitation of this approach is that
the abstracts associated with a gene and processed into a
vector must be provided to the system.
Shatkay et al., (2000) developed a theme extraction system
for large-scale gene analysis. A theme was derived
from a set of MEDLINE abstracts with similar term distributions.
The abstract set was obtained from a user-provided
kernel document known to be about a particular
gene, but from that kernel the system obtained similar documents from MEDLINE automatically, using a standard
cosine-based similarity metric. The resulting set was
then processed to extract “executive summary” terms defining
the theme of the abstract set and, hence, the gene
behind it. Theme similarity between two genes was based
on the members shared by the themes of their two corresponding
abstract sets. The final results included, for each
gene, a theme consisting of characteristic terms and a list
of the most similar genes. A limitation of the system is its
dependence on the kernel documents, which the user must
provide. For microarray experiments involving a large
number of genes, the time and effort required to identify
kernel documents might be prohibitive even when good
The “literature profiling” system of Chaussabel and Sher,
(2002) also found gene clusters based on text clustering.
The system represented genes as vectors of keywords extracted
from MEDLINE abstracts. The vectors were then
clustered using a software package originally developed
for gene-expression profiling. The resulting clustergram
showed gene clusters with similar keyword profiles. The
genes in a cluster were interpreted as functionally related.
This text clustering-based approach avoids a significant
limitation of the approach of Shatkay et al. and Chagoyen
et al. in that the burden of providing hand-selected documents
is avoided (although they mention that providing
PubMed queries that produce good document sets can be
non-trivial). However, literature profiling has its own limitations.
||The algorithm was originally developed for gene expression
clustering, not keyword clustering, and performed
poorly on high-dimensional vectors. The authors
were forced to filter the keywords aggressively
to reduce the dimensionality, retaining just 101 out of
25,000 terms, a significant loss of information.
||The clusters were dominated by well-studied genes
with rich keyword profiles, because they were mentioned
in many abstracts. Newly discovered or lessstudied
genes had only a few abstracts and so were
relatively neglected because of their sparsely populated
||The system only counted unigrams. Thus functional
information in multiple-word terms was left unused.
For example, the meaning of “red blood cell” is difficult
to capture from the separate words “red,” “cell”
and “blood” scattered among many other keywords.
Although the Chagoyen et al., (2006); Shatkay et al., (2002); and
Chaussabel and Sher, (2002) systems avoided the inherent shortcomings of assuming that genes with similar expression
patterns are involved in the same functional pathways,
they still required facing the significant challenges of effectively
extracting, processing and presenting functional
information from free text.
Glenisson et al., (2003) addressed this issue with an approach
similar to the literature profiling of Chaussabel
and Sher, (2002) but with the following significant differences.
||Each gene’s functional description was collected from
the Saccharomyces Genome Database and the SWISSPROT
database, supplemented with 20 MEDLINE abstracts.
But this requires data availability, limiting the
analysis to well-studied genes.
||The functional descriptions were represented in a predefined
vector space of GO concepts.
Because of its reliance on GO, limitations of GO as
discussed above apply to this system, e.g., its unbalanced
development and incomplete coverage. This tends to counteract
the objective of using the literature to obtain the
most comprehensive and up-to-date functional information.
|We created a new system architecture which addressed
limitations of the above-mentioned tools with an approach
based on two clustering stages. The feasibility of this
architecture was tested by building an example system,
GeneNarrator, based on it. There are five requirements
which the architecture meets.
1. Intended application
|The architecture is intended for functional interpretation
of microarray experiments for which information
exists in the literature about the genes involved. However,
with modest modification, it should be adaptable to
proteomic and metabolomic data as well.
|Input should be as simple as possible — for example, a
list of gene names.
3. Source of functional information
|Functional information should be obtained from
MEDLINE abstracts, since they are fairly comprehensive
and up-to-date. Functional annotations in public genomic
databases tend to cover well-studied genes in model organisms,
so depending on them would have made the architecture inapplicable to less-studied genes or non-model
organisms. Avoiding reliance on these sources also avoids
concerns about annotation errors and update delays.
4. Algorithmic constraints
|The analysis should provide a summarized picture of
the thousands or even tens of thousands of MEDLINE
abstracts that may be collected for a given list of genes.
Text clustering is a natural choice, because it can divide a
large number of documents into groups based on topic
differences (usually based on similarities in word content).
The clustering solution should be designed to avoid
the pitfalls illustrated in some of the above-reviewed systems.
||Well-studied genes with many abstracts should not
dominate the clustering process to the relative neglect
of newly discovered or less-studied genes.
||Hierarchical clustering algorithms are more suitable
than flat ones. Users rarely know beforehand how
many clusters should be in the final result. With hierarchical
clustering, the number of clusters is relatively
flexible, as branches can be merged after the analysis.
||The text-clustering algorithm of choice should perform
well in high-dimensional vector spaces.
||Multiple-word terms should be incorporated in text
clustering. Many biomedical concepts are multiword
terms. Breaking them down to unrelated single words
may adversely affect clustering results, because useful
information is lost.
5. Output of results
|Results of an analysis should include a hierarchical structuring
of topics, the biological meanings of the topics,
and how many and what genes are in what topics.
The Algorithms, Architecture and Implementation
|A two-stage clustering approach was designed for
GeneNarrator to use to provide functional summarizations
of microarray experiments from information in MEDLINE
(Fig. 1). The system is designed to take as input a userprovided
gene list, and automatically queries PubMed for
abstracts mentioning one or more of the genes. Gene symbols,
official names, synonyms and gene product names
could potentially all be included to retrieve more relevant
abstracts. PubMed uses a sophisticated query expansion
method to increase the recall of relevant records. However,
increased recall in general tends to reduce precision.
This is an issue with most systems that use information
retrieval rather than hand-curated data sets as input. An
example of this specific to the gene annotation problem is
ambiguous gene names, which tend to occur most in the
most widely studied organisms. The precision will depend
heavily on the particular gene list.
Figure1: Functional overview of GeneNarrator.
The system is designed to group the pool of retrieved
abstracts into functional topics using a text clustering algorithm.
Next, each gene is associated with the distribution
of its occurrences across the set of topics, i.e., a vector stating its number of occurrences in the MEDLINE
records comprising each topic. Then, a second clustering
stage groups genes with similar distributions.
GeneNarrator, the name of the demonstration implementation,
consists of six modules: DocBuilder, LongBOW
(BOW from “Bag Of Words”), CrossBOW, GeneSmith,
ArrowSmith (not related to the Arrowsmith system, http://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html),
and BOWviewer (Fig. 2). DocBuilder retrieves MEDLINE
abstracts that are related to at least one of the user-provided
genes. LongBOW performs several preprocessing
tasks on the abstracts, including discarding stopwords,
stemming, and detecting multiple-word terms. CrossBOW
clusters the abstracts into a hierarchy of functional topics.
ArrowSmith extracts representative keywords from
CrossBOW’s output, and scores keyword-containing sentences
and abstracts. The keywords and high-scoring sentences
and abstracts are intended to help in interpreting the
biological meanings of the topics. GeneSmith calculates,
for each gene, a distribution describing its occurrences
across the topics, then clusters the genes with similar distributions.
BOWviewer is a GUI for navigating the hierarchical
topics, browsing the representative keywords, sentences
and abstracts, and comparing the topic distributions
of individual genes or gene clusters. All modules were
implemented in Java, except CrossBOW which is in C.
Figure 2: Architectural overview of GeneNarrator.
|Here we give additional details about the design of the
various modules of GeneNarrator, as it may be of interest to future system builders.
Document retrieval (DocBuilder)
|Given a file containing a list of genes, one gene per
line, the DocBuilder module retrieves MEDLINE abstracts
related to each of the genes via eUtils, which are the Entrez
Programming Utilities (National Library of Medicine
2004). DocBuilder is designed to hold four submodules,
the querier, sampler, fetcher and parser. The querier
embeds a gene name, together with its synonyms and gene
product names if provided, into a query which it sends to
PubMed using the eUtils ESearch function. PubMed returns
a list of PMIDs. A user may set an upper limit for
the number of PMIDs to be used in the subsequent processing
steps. If the number of returned PMIDs exceeds
the upper limit, the sampler draws a random sample from
the list. The returned or sampled PMIDs are recorded in a
gene-to-PMID map file for later use. The fetcher then retrieves
the PMIDs’ full abstracts from PubMed using the
eUtils EFetch function. Finally, the parser extracts the
titles and the abstracts from the retrieved abstracts, and
writes them to plain text files. The submodules we built
for our demonstration system, GeneNarrator, were used
earlier in MedKit (Ding and Berleant, 2005), and PubMed
Assistant (Ding et al., 2006).
|The LongBOW module preprocesses the MEDLINE
abstracts in order to get better clustering results. The preprocessing
was designed to perform the following steps.
||Remove stop words, such as “that,” “is,” “you,” and
“of.” A user-defined stopword list can replace the default
||Perform stemming. For example “regulation,” “regulating,”
“regulator,” and “regulates” are all stemmed
to “regulat.” The stemming method is a Java implementation
(http://www.tartarus.org/martin/PorterStemmer/) of the Porter, (1980) stemming algorithm.
||Detect and label multiple-word terms (MWTs).
Detecting and labeling MWTs is done in three passes
through the abstracts. The first pass performs stopword
removal and stemming. Also, for each unique single-word
term (SWT), its df (document frequency, or number of
documents containing the term) and tf (term frequency, or
total number of appearances of the term in the entire document
set) are counted. The total number of tokens (words,
including stopwords, and punctuation marks) is also recorded.
After the first pass, a threshold value is used to
separate out SWTs that are significant, defined as having
a df above the threshold.
In the second pass, unique double-word terms (DWTs)
are counted. A DWT is defined as two consecutive SWTs
without any intervening stopwords or punctuation. Both
constituent SWTs must be above the df threshold. A
DWT’s observed count is tested against the null hypothesis
that two SWTs are next to each other by chance. The
test is similar to the “t-test” of collocations described by
Manning and Schultze, (1999). Briefly, let the number of
occurrences of single-word term wi in the entire document
(in this case, abstract) be ni, the total number of tokens
(words and punctuation marks) in the document set
be N, and the number of occurrences of double-word term w1w2 be n12. Then the probability of an occurrence of w1 being followed by w2 under the null hypothesis is p=n2 /N, and the expected number of occurrences of w12 is nexp=n1p. We can construct an approximate binomial test by z = n12 - nexp / √n1p(1-p) and use tables for z from many standard
statistics texts to decide whether or not to reject the
null hypothesis. DWTs for which the null hypothesis is
rejected are significant.
In the third pass, significant DWTs are evaluated in the
context of individual MEDLINE abstracts if their two
constituent SWTs are mentioned a similar number of times
in the abstract. For example, an occurrence of “cell cycle”
would not be used as a DWT in a abstract that mentioned the word “cell” 10 times, but the word “cycle” only once.
Even though “cell cycle” might appear more frequently
than expected by chance in the entire abstract set, it would
not be deemed a major subject in that abstract. Formally,
given a significant DWT w1w2 with corresponding constituent
SWT term frequencies tf1 and tf2 in a abstract, and a predefined threshold α > 1, the DWT is used if and only if 1/α £ tf1 / tf2 α, where α is the sensitivity. Too high
a sensitivity will tend to lead too high a vector space dimensionality,
which will likely decrease the quality of the
clustering for typical data sets. This study used an α value
Finally, MWTs are detected if DWTs chain together.
Upon detecting a qualified DWT, LongBOW replaces the
space with an underscore character (e.g., cell_cycle). This
trick enables CrossBOW to treat the DWTs and MWTs as
Text clustering (CrossBOW)
|The CrossBOW module was modified from the open
source “Bow” toolkit (McCallum, 1996). Its clustering
algorithm, the Cluster-Abstraction Model (CAM)
(Hofmann, 1999), was designed specifically for text clustering.
A CAM consists of a vocabulary, and many topics
that are automatically extracted and organized as nodes
in a hierarchical tree. Each topic is defined by a vector of
probabilities Pt. Each probability in the vector is the likelihood
of the topic containing a certain word from the
vocabulary. Each leaf topic has a unique path to the root
of the tree. The topics along the path are considered to be
different abstraction levels. The closer to the root, the
higher the abstraction level. There is a document bin for
each route. This bin, like a topic, is also associated with a
vector of probabilities Pb. Each probability is the likelihood
of the bin producing documents from a certain abstraction
level. Finally, the entire model has a vector of
probabilities Pm, each giving the likelihood of the model
producing documents from a certain bin.
Given a model, a set of documents can be generated by
iteratively picking a bin according to Pm, picking an abstraction
level (that is, a topic) according to Pb given the
bin, and producing words according to Pt given the topic.
Clustering a set of documents is equivalent to finding the
hierarchical topic structure and associated probabilities
with the maximum likelihood of generating that set of
documents. Compared to other distance-based algorithms,
especially agglomerative clustering methods, CAM has
the following advantages (Rose et al., 1990):
||insensitivity to term-weighting methods and distance (similarity) definitions,
||a statistically sound foundation,
||multiple levels of text clustering,
||representative keywords for topics, and
||efficient model fitting by annealed expectation maximization.
CrossBOW clusters a set of documents (in plain text
format) into a hierarchical topic tree. Each document is
assigned to one and only one of the nodes (topics). The
branching factor and maximum depth of the tree are designed
as command line options. The modifications to
CrossBOW introduced for GeneNarrator include:
||recognition of multiword terms labeled by LongBOW,
||addition of a command line option to change the number
of topic keywords in the output.
Interpreting the topics biological meanings
|Given the hierarchical topics and the representative topic
keywords generated by CrossBOW, the ArrowSmith module
is designed to score the sentences and the abstracts
containing them. Each topic-representative keyword is
assigned a keyword score. For example, the binary scoring method gives all representative keywords a score of
one. Other scoring methods could assign different scores
to different keywords based on their probabilities or ranks.
A sentence’s score is the sum of its keyword’s scores, and
an abstract’s score is the sum of its sentence’s scores. The
representative keywords and the highest-scoring sentences
and abstracts define the inferred biological meaning of
Gene-to-topic mapping and clustering (GeneSmith)
|The GeneSmith module is designed to convert the abstract
set associated with a particular gene into a topic
distribution by straightforwardly counting how many abstracts
in the set fall into each topic. It then clusters genes
based on the similarities of their distributions across topics.
The clustering algorithm may be chosen as either kmeans
or expectation maximization (EM) from the Weka
machine-learning workbench (Frank et al., 2004).
Result browsing (BOWviewer)
|The BOWviewer module (Fig. 3) is a graphical user
interface built for browsing the results. It shows the
topic hierarchy (left), the representative keywords (top),
high-scoring sentences or abstracts for each topic (middle),
and other information. Users can readily navigate through
the hierarchical topic tree. They can browse topic keywords,
high-scoring sentences, and abstracts, and they can
annotate the topics with biologically meaningful comments. Users can also check the genes associated with a
particular topic (e.g. topic 7 in Fig. 3., lower middle), and the
topics and their strengths (lower right corner) associated
with a highlighted gene in the gene list (lower middle
Figure 3: BOWviewer user interface.
|To validate the architecture we performed an experiment
on a list of 155 yeast genes (Table 1) manually selected
from ten pathways in the comprehensive yeast genome
database (Munich Information Center for Protein Sequences,
2006). Care was taken in picking the pathways
so that the overlap was low, though some overlap was
unavoidable. The modules were run with the following
command line parameters.
Table 1: Hand-picked genes from the Comprehensive Yeast Genome.
||maximum number of abstracts per gene = 50
||single word term df (document frequency) threshold
||double word term p value = 0.025
||double word term tf (term frequency) ratio = 3.0
||default stopword lists
||branching factor = 2
||maximum branch depth = 4
||number of output keywords per topic = 50
||scoring method = binary
||number of top-scoring sentences and abstracts = 25
||clustering algorithm = k-means
||k = 15
DocBuilder retrieved 2,819 abstracts from MEDLINE,
some of which covered two or more genes in the list.
CrossBOW was used to generate a topic hierarchy organized
as a binary tree. It then assigned each abstract to
one of the 32 leaf nodes. Each node was associated with
50 keywords, as well as 25 top-scoring sentences and abstracts
(helpful in grasping the node’s biological meaning).
For example, the keywords for topic 0/0/0/0/0 (Table
2) strongly suggest proteolytic activities, which would be
expected for the genes from the ubiquitin-mediated proteolytic
pathway. The majority of the topic’s MEDLINE
records (102 of 119) came from the pathway’s member
genes; and the genes contributed most of their MEDLINE records (102 out of 138) solely to the topic. Other genes’
abstracts were more broadly distributed among the topics.
For example, some genes from the respiratory chain
pathway contributed their abstracts mainly to two or three
closely related topics (e.g. 1/0/0/0/0, 1/0/0/0/1 and 1/0/0/1/0), corresponding to mitochondrial genome, mitochondrial
protein biosynthesis and mitochondrial ATP biogenesis,
respectively (Table 3).
Table 2: Representative keywords, and contributing genes and groups, for topic 0/0/0/0/0.
*G enes contributing only 1 citation to the topic were omitted.
Table 3: Topic distributions of some genes from the respiratory chain pathway.
*O ther topics with 1 or 2 abstracts were omitted.
The GeneSmith module clusters genes into groups based
on their topic distributions. This is the second stage of
the novel 2-stage clustering process of our architecture.
For example, four of the genes listed in Table 3 (Q0045,
Q0105, Q0250, and Q0275) were assigned to the same
group because of their similar distributions in topics 1/0/0/0/0 and 1/0/0/0/1. Although Q0130 was from the same
pathway, it was clustered into another group because a
significant portion of its abstracts contributed to topic 1/0/0/1/0. Even though this topic is related to the above
two topics, the clustering algorithm (k-means) did not use
this fact. The algorithm also seemed sensitive to details.
For example, while a human expert would probably group
the six major contributing genes of topic 0/0/0/0/0 into a
single cluster, the algorithm assigned them into three clusters
(groups 7, 8 and 11 in Table 2), because their contributions
ranged from 43% to 100%. Other clustering algorithms
and weighting methods might improve the second
clustering stage. Nevertheless, the system is robust to
noise introduced throughout the process in that the results
make sense despite that noise.
Discussion and Conclusion
Two-stage vs. one-stage clustering
|The two-stage clustering approach, in which first
MEDLINE abstracts are clustered, and those clusters are
then used as input to the gene clustering stage, is a distinguishing
feature of the architecture and its example implementation,
GeneNarrator. The two stage design overcomes
three significant drawbacks of basic single-stage clustering:
||the dominance of well-studied genes over less-studied
||the dilemma of assigning less-studied genes to the right
||the difficulty of grasping clusters’ biological meanings.
Some genes are well studied, with hundreds, even thousands
of hits in MEDLINE. Newly discovered and less
popular genes may have only a few hits. In a basic onestage
clustering design, each gene is represented by the
set of its abstracts. When directly compared, genes with
many abstracts will have a strong tendency to dominate
genes with only a few. This was vividly illustrated for
example by Chaussabel and Sher, (2002, figure 2). This is
a problem that needs to be addressed. The two stage design
of GeneNarrator avoids this dominance problem because
the number of abstracts for a gene does not translate into a corresponding degree of influence in the ultimate
clustering of genes. Consequently all abstracts count,
regardless of whether they discuss a gene with many other
abstracts or one with only a few. This is an advantage of
the two stage design as compared to a basic one stage
design. Alternatively, a one-stage approach might be
adopted which does some form of averaging so that gene
representations do not expand without restriction as they
become more studied. For example, the semantic attribute
approach of Chagoyen et al., (2006) is in this paradigm.
Many genes, especially well-studied ones, are on record
as participating in multiple pathways. Texts mentioning
such genes may therefore contain keywords indicative of
any of these pathways. In a one-stage clustering design
an individual topic cluster dominated by well-studied
genes may therefore discuss multiple pathways. Furthermore,
sets of pathways discussed in different topic clusters
may overlap. This overlap can make assigning a lessstudied
gene or other gene discussed in the context of a
single pathway to a cluster a dilemma. On the one hand,
it must be assigned to at least one of the overlapping clusters
discussing its pathway. On the other hand, it is problematic
to assign it to any of those clusters, because membership
in a multi-pathway cluster seems to suggest potential
relevance to more than one pathway. In the twostage
approach, this problem is less likely. During the
first stage, text clustering may group abstracts into
topics containing more than one pathway, and one pathway
may end up in more than one topic. But the second,
gene clustering stage permits assigning less-studied genes
to individual pathways, while well-studied genes can be
assigned to multiple topics simultaneously.
Finally, each topic cluster should be annotated, such as
with a list of representative keywords, sentences, etc. From
a user’s perspective, it will typically be easier to grasp the
biological meaning of a gene cluster from keyword and
sentence annotations associated with it, if it contains truly
Availability and Requirements
|System developers may wish to incorporate two-stage
clustering and other aspects of the architecture discussed
in this paper into their own systems. Alternatively, the
code we developed is available to use as a starting point.
The official project Web site URL is http://bioinformatics.ualr.edu/dan/genenarrator/. Links are provided
for downloading source code, a zip package, a
sample data set, and the user manual. Linux is needed as
CrossBow requires it, however, other components can run
under other platforms. One GB is required for moderately-sized data sets (~500 genes/proteins/metabolites or
~10,000 MEDLINE abstracts).
|This work was supported in part by The Procter and
Gamble Company. We are grateful for the comments of
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