In these exercises, we will use a variety of text-mining tools and databases based on text mining to interpret the results from microbiome studies. The exercises will teach you how to:
- automatically highlight named entities in a web page
- use named entity recognition for synonym-aware information retrieval
- extract associations based on cooccurrence of entities in the literature
- discover novel, indirect associations between entities
- perform text-mining-based term enrichment analysis
All exercises are purely web-based.
In this exercise we will first introduce the basics of text mining: 1) dictionary-based named entity recognition and 2) how this can used to help retrieve literature. Afterwards we will move on to how one can use the complete literature to 3) extract associations between entities and finally 4) how these associations can be used for knowledge discovery.
1.1 Named entity recognition
The goal of named entity recognition (NER) is to find names mentioned in text and resolve them to the underlying biomedical entities (document → A, B, C). To illustrate this, we will use the EXTRACT tool, which is designed to use NER to support manual database curation.
Install the EXTRACT bookmarklet as described on the EXTRACT website.
Open the paper “Intestinal Microbiota and the Efficacy of Fecal Microbiota Transplantation in Gastrointestinal Disease” (Aroniadis et al., 2014) and click the EXTRACT bookmarklet. After a short time, terms should be highlighted in the text.
What do the different colors mean?
By clicking or hovering over a tagged term, you will get a popup that includes its standard name, entity type, database or ontology identifier, and a link to its reference record. Click or hover over pseudomembranous colitis and Micrococcus pyogenes.
What is an alternative name for pseudomembranous colitis? What is the difference between Micrococcus pyogenes and Staphylococcus aureus?
Select the Keywords line in the paper and click the EXTRACT bookmarklet. Hover over terms in the text or lines in the table.
Use the buttons in the popup to copy the data into a spreadsheet/text file or save it in tabular format.
Which information is then provided in addition to what is shown in the popup?
1.2 Information retrieval
The goal of information retrieval (IR) is to find the documents pertaining to a topic of interest. When the topic is a biological entity (A), NER can be used to index the literature and thereby support retrieval of relevant documents (A → documents).
We run the same NER system used in EXTRACT on entire PubMed every week and make the results available through a suite of web resources. One such resource is ORGANISMS. It allows users to retrieve abstracts that mention any organism of interest (specified by an NCBI TaxID) based on the NER results.
Go to https://organisms.jensenlab.org/ and query for S. aureus. You are now presented with several options, since there are many genera starting with S that include an aureus species. Click on the Staphylococcus aureus (taxid:1280) row to view the abstracts for this species.
Do the abstracts shown all mention Staphylococcus aureus?
Go back to the search page (e.g. by clicking ORGANISMS in the header) and query for Firmicutes. You are again presented with many options including the Firmicutes phylum itself (taxid:1239) as well as numerous species and strains. Click on the row for the phylum to view abstracts.
Which taxa do you see abstracts for?
You can similarly use NER to retrieve abstracts for any disease in the Disease Ontology. For example, the following query will retrieve abstracts for inflammatory bowel disease (DOID:0050589):
Which diseases are highlighted in the abstracts?
1.3 Information extraction
The goal of cooccurrence-based information extraction (IE) is to link entities (A, B, C) to each other based on them being mentioned together in documents (A → documents → B; B → documents → C).
Go to https://diseases.jensenlab.org/ and query for Crohn disease. Again, click on it on the disambiguation page (like in the ORGANISMS resource).
Which gene is most strongly associated with Crohn’s disease according to text mining?
Click on NOD2 in the text-mining table.
Do the abstracts in fact support an association between Crohn’s disease and NOD2?
Cooccurrence-based IE is a very generic approach, which can be used to find associations between any two types of entities for which we can do NER. For example, we can use the same approach to link Staphylococcus aureus together with the gene NOD2:
1.4 Knowledge discovery
The goal of knowledge discovery is to find indirect associations between entities (A, C) via other entities (B). In the so-called closed discovery problem, we search for B entities that can explain an observed association between A and C (A → B ← C), which may never have been mentioned together in the literature. For example, we saw above that both Crohn’s disease and Staphylococcus aureus have links to NOD2, which could mechanistically explain an observed association between Staphylococcus aureus and Crohn’s disease.
ARROWSMITH is a tool for discovering such associations in a systematic manner; its Two-Node Literature Search corresponds to the closed discovery problem.
Open ARROWSMITH and do a basic two-node literature search using Staphylococcus aureus as A-literature and Crohn’s disease as C-literature. After some minutes you should see a ranked list of B-terms that were mentioned in both the A-literature and the C-literature.
Which is the top-ranking B-term?
Inspect some of the literature supporting the A–B and the B–C associations.
Does B provide a plausible connection between A and C?
In this exercise, we will focus on how one can utilize the text-mining tools used in exercise 1 to interpret the results from a microbiome analysis. To this end, we will start from the results published on the human colorectal cancer microbiome (Zeller et al., 2014).
It is important to note that there are currently no dedicated text-mining tools that have been designed to aid microbiome analysis. What we will do is thus to (ab)use existing text-mining tools and resources, to illustrate what is already now possible with text-mining and which will hopefully be possible to do in a more user-friendly manner in the future.
2.1 Using NER to dig deeper
Colorectal cancer studies have revealed a strong cooccurrence pattern between the proinflammatory Fusobacterium nucleatum and Parvimonas micra. This led to a systematic search for literature linking also the latter bacterial species to inflammatory response. A simple PubMed search retrieves only three publications:
Of these, only one had been published when the colorectal cancer microbiome was being analyzed, and it sheds no light on the topic. However, since Parvimonas micra has an NCBI Taxon ID (taxid:33033) and inflammatory response is a GO term (GO:0006954), we can instead use the results of NER to retrieve relevant documents:
Because NER makes use of synonyms, this retrieves several additional publications. Inspect these abstracts.
Are they relevant and why were they were not found by the initial search?
One of the abstracts (Yoshioka et al., 2005) reveals a possible link between the two bacteria and oral inflammatory response: Parvimonas micra can bind to lipopolysaccharides on Gram-negative bacteria such as Fusobacterium nucleatum and thereby induce inflammatory response. This publication was missed by the PubMed query, because Parvimonas micra is referred to under its older name Peptostreptococcus micros. The species is thus mentioned, but a search for its current name will not retrieve it.
Open the abstract by Yoshioka et al. in PubMed and run EXTRACT on it. Inspect the tagging of Peptostreptococcus micros.
Which name is listed for the species in the popup?
2.2 Linking taxa to diseases
Above, we saw how existing text-mining resources can be used to retrieve abstracts that mention a species of interest with a disease of interest. Very similar to the previous exercise, we can easily look up the abstracts that mention, for example, Fusobacterium nucleatum (taxid:851) together with colorectal cancer (DOID:9256):
Is this association supported by only few papers or is it well established in the literature?
To do this systematically for all taxa found in a microbiome study, automation is desirable. One could obviously partially automate this by producing a web page with links like the one above for a list of organisms. Alternatively, one can download the full results from named entity recognition and write a simple script to identify all abstracts that mention organisms of interest with diseases of interest, which can then serve as a starting point for either manual curation of the associated articles or statistical analyses.
2.3 Microbiome characterization
Already prior to the microbiome study analyzed here, it had been noted that several bacteria associated with colorectal cancer were first described as oral pathogens. It had also been suggested that their invasion of the gut might cause or contribute to tumorigenesis (Warren et al., 2013). We will explore this in a systematic manner by investigating the text-mined associations between bacteria identified in the colorectal cancer microbiome study and tissues.
In that context, simplest possible characterization is to just count how many of the bacteria associated with colorectal cancer can be associated with each tissue (BTO term) through text mining. To perform such an analysis, go to the SimpleCount web server. As Foreground paste in the list of NCBI TaxIDs corresponding to the bacteria of interest; we have prepared a file with the colorectal cancer-associated NCBI TaxIDs. Next select the Dictionary that you want counts for (i.e. Tissues), specify a Z-score cutoff for the text-mining association (leave at default for now), and click the Count button. After a few seconds, you will see a table with the results of the analysis; you can sort the table by clicking on the column headings.
Which are the most frequent tissue terms? Are these terms specific of very broad?
Go back to the input page, lower the Z-score cutoff to 3.0 and rerun the analysis.
How does this change the results?
The SimpleCount server also allows you to count terms in both a foreground and a background set of organisms and test each tissue term for statistically significant overrepresentation in the foreground set. This type of analysis yields terms that are frequent in the foreground set but not in the background set, as opposed to the terms identified above, which are merely frequent in the foreground set. To perform this analysis use the same Foreground set as in the previous analysis, paste in the full list of bacteria identified in the study into Background, set the Z-score cutoff to 5.0, set the P-value cutoff to 0.001, and click Count. The results table now includes two additional columns, namely the background count and the p-value. Note that the reported p-values are not corrected for multiple testing.
Are the enriched terms more specific than those with the highest counts?
These types of analyses are by no means limited to tissues. If the task asks for it, equivalent analyses can be done for, e.g., diseases or environmental descriptors. Perform an enrichment analysis for diseases using a Z-score cutoff of 4.0. The slightly lower cutoff reflects that the text-mined associations between diseases and organisms are not quite as strong as those between tissues and organisms.
Which are most significantly enriched diseases?
2.4 Mining for indirect associations
After Fusobacterium nucleatum, the most overrepresented bacterial species in samples from colorectal cancer patients is Peptostreptococcus stomatis. A search for abstracts linking Peptostreptococcus stomatis to colorectal cancer retrieves a few publications; however, none of these shed any light on the association:
Use ARROWSMITH to search for B-terms that connect the A-term Peptostreptococcus stomatis to the C-term colorectal cancer. Look through the list of suggested B-terms.
Most of the top terms are very general terms related to microbiome sequencing. However, multiple terms related to oral squamous cell carcinomas are also found to be linked both to the species in question and to colorectal cancer. Inspect the underlying literature for this indirect association in ARROWSMITH.
Does this indirect association appear to hold up to closer scrutiny?
Similarly, query ARROWSMITH for terms connecting Lactobacillus ruminis to colorectal cancer. This should suggest inflammation as a possible (if somewhat vague) connection between the two.