Identifying genotype-phenotype relationships in biomedical text

Identifying relationships between biomedical entities by analyzing only biomedical text

Finding the relationships between entities from information contained in the biomedical literature has been studied extensively and many different methods to accomplish these tasks have been proposed. Generally, current approaches can be divided into three types: Computational linguistics-based (e.g., [2–4]), rule-based (e.g., [5, 6]), and machine learning and statistical methods (e.g., [7, 8]). Furthermore some systems (e.g., [9–11]) have combined these approaches and have proposed hybrid methods.

RelEx [10] makes dependency parse trees from the text and applies a small number of simple rules to these trees to extract protein-protein interactions. Leroy et al. [12] develop a shallow parser to extract relations between entities from abstracts. The type of these entities has not been restricted. They start from a syntactic perspective and extract relations between all noun phrases regardless of their type. SemGen [9] identifies and extracts causal interaction of genes and diseases from MEDLINE citations. Texts are parsed using MetaMap. The semantic type of each noun phrase tagged by MetaMap is the basis of this method. Twenty verbs (and their nominalizations) plus two prepositions, in and for, are recognized as indicators of a relation between a genetic phenomenon and a disorder. Sekimizu et al. [2] use a shallow parser to find noun phrases in the text. The most frequently seen verbs in the collection of abstracts are believed to express the relations between genes and gene products. Based on these noun phrases and frequently seen verbs, the subject and object of the interaction are recognized.

Coulet et al. [4] propose a method to capture pharmacogenomics (PGx) relationships and build a semantic network based on relations. They use lexicons of PGx key entities (drugs, genes, and phenotypes) from PharmGKB [13] to find sentences mentioning pairs of key entities. Using the Stanford parser [14] these sentences are parsed and their dependency graphs¹ are produced. According to the dependency graphs and two patterns, the subject, object, and the relationship between them are extracted. This research is probably the closest to the work presented here, the differences being that the method to find relationships is rule-based and the entities of interest include drugs. Direct comparison with our results is difficult because the genotype-phenotype relationships with their associated precision and recall values are not presented separately. Temkin and Gilder [3] use a lexical analyzer and a context free grammar to make an efficient parser to capture interactions between proteins, genes, and small molecules. Yakushiji et al. [15] propose a method based on full parsing with a large-scale, general-purpose grammar.

The BioNLP module [5] is a rule-based module which finds protein names in text and extracts protein-protein interactions using pattern matching. Huang et al. [6] propose a method based on dynamic programming [16] to discover patterns to extract protein interactions. Katrenko and Adriaans [8] propose a representation based on dependency trees which takes into account the syntactic information and allows for using different machine learning methods. Craven [7] describes two learning methods (Naïve Bayes and relational learning) to find the relations between proteins and sub-cellular structures in which they are found. The Naïve Bayes method is based on statistics of the co-occurrence of words. To apply the relational learning algorithm, text is first parsed using a shallow parser. Marcotte et al. [17] describe a Bayesian approach to classify articles based on 80 discriminating words, and to sort them according to their relevance to protein-protein interactions. Bui et al. [11] propose a hybrid method for extracting protein-protein interactions. This method uses a set of rules to filter out some PPI pairs. Then the remaining pairs go through a SVM classifier. Stephens et al. [18], Stapley and Benoit [19], and Jenssen et al. [20] discuss extracting the relation between pairs of proteins using probability scores.

Supervised learning approaches have been used to recognize concepts of prevention, disease, and cure and relations among these concepts. Work using a standardized annotated corpus beginning with Rosario and Hearst [21] and continuing with the work of Frunza and Inkpen [22, 23] and Abacha and Zweigenbaum [24, 25] has seen good performance progress.

An approach to extract binary relationships between food, disease, and gene named entities by Yang et al. [26] has similarities to the work presented here because it is verb-centric.

Most of the biomedical relation extraction systems focus on finding relations between specific types of named entities. Open Information Extraction (OIE) systems aim to extract all the relationships between different types of named entities. TextRunner [27], ReVerb [28], and OLLIE [29] are examples of OIE systems. They first identify phrases containing relations using part-of-speech patterns and syntactic and lexical constraints, and then with some heuristics detect related named entities and relation verbs. PASMED [30] extracts diverse types of binary relations from biomedical literature using deep syntactic patterns. Advanced OIE systems [31, 32] have been proposed to extract nominal and n-ary relations.

Increasing interest in neural network models, such as deep [33], recurrent [34], and convolutional [35] networks, and their applications to Natural Language Processing, such as word embeddings [36] have provided a new set of techniques for relationship identification, some which deal with relationships of a general nature, such as Miwa and Bansal [37], and some which deal with biomedical relationships, such as Jiang et al. [38]. Our method is a more traditional pipeline method—identifying genotypes and phenotypes, and then using surface, syntactic, and dependency features to identify the relationships. So, rather than developing an extensive overview of these neural network models, we instead point the reader to Liu et al.’s excellent summary of these methods [39].

Identifying genotype-phenotype relationships using biomedical text and/or other curated resources

The research works mentioned in the previous section have been highlighted because they are concerned with identifying various relations among biomedical entities by analyzing only the natural language context in which mentions of these relations and entities are immersed. There is a vast literature presenting research focussed specifically on the genotype-phenotype relation. Most of this research presents the discovery of novel genotype-phenotype relations based on biomedical evidence and is beyond the intent of this paper and would be out of place to be surveyed here. Incidentally, it is this type of literature that we are interested in mining to extract genotype-phenotype relationships.

While not finding genotype-phenotype relationships, many research works are concerned with a related question: disease-gene relationships. One of the earliest works in this area is that of Doughty et al. [40] which provides an automated method to find cancer- and other disease-related point mutations. The method of Singhal et al. [41] to find disease-gene-variant triplets in the biomedical literature makes strong use of a number of modern natural language tools to analyze the text in which these triplets reside, but this method also uses information mined from all of the PubMed abstracts, the Web, and sequence analysis which requires the use of a manually curated database. Another research work that investigates gene variants and disease relationships is that of Verspoor et al. [42]. Another work that investigates mutation-disease associations is Mahmood et al. [43]. A recent review of algorithms identifying gene-disease associations using techniques based on genome variation, networks, text mining, and crowdsourcing is provided by Opap and Mulder [44].

Other literature reports on techniques to extract genotype-phenotype relationships combining biomedical text mining with a variety of other resources. An example of this type of technique is the pioneering work of Korbel et al. [45]. Being the first to use evidence from biomedical literature, it uses the correlation of gene and phenotype mentions in the text together with comparative genome analysis that depends on a database of orthologous groups of genes to provide gene-phenotype relationship candidates. Novel relationships that were not mined directly from the text are reported. Another type of technique, exemplified by the work of Goh et al. [46] is the integration of curated databases to find genotype-phenotype relationship candidates.

A work by Bokharaeian et al. [47] which is very close to the research presented here uses two types of Support Vector Machines for their learning method and the type of relationship being identified is between single-nucleotide polymorphisms (SNPs) and phenotypes. This work presents three types of association (positive, negative, and neutral) and three levels of confidence (weak, moderate, and strong).

In each of the referred to works, either the presentation of the genotype-phenotype relationship is complicated by being part of a larger relationship, such as in the work of Coulet et al. [4], or the method to suggest the relationship requires information found in manually curated databases, such as the works of Korbel et al. [45], Goh et al. [46], and Singhal et al. [41]. Our work then stands out by being different on each of these fronts: we identify only the genotype-phenotype relationships and we use only the text in the PubMed abstract being analyzed. Also, we are not attempting to find new relationships, rather we are only mining those relationships that occur in the abstract. In addition, we are using a machine learning method that requires human annotated data. We view the method provided in this paper as complementing these other methods in the ways just described.

Briefly then, in this paper we discuss a semi-supervised learning method for identifying genotype-phenotype relationships from biomedical literature. We start with a semi-automatic method for creating a small seed set of labelled data by applying two named entity relationship tools [48] to an unlabelled genotype-phenotype relationship dataset. This initially labelled genotype-phenotype relationship dataset is then manually cleaned. Then using this as a seed in a self-training framework, a machine learned model is trained. It is worth noting that throughout this paper we do not take into account the phenotypes at the subcellular level. The evaluation results are reported using precision, recall and F-measure derived from a human-annotated test set. Precision (or positive predictive value) is the ratio of correct relationships in all relationships found and can be seen as a measure of soundness. Recall (or sensitivity) is the ratio of correct relationships found compared to all correct relationships in the corpus and can be used as a measure of completeness. F-measure combines precision and recall as the harmonic mean of these two numbers.

Semi-supervised learning

To train machine learning systems, it is easier and cheaper to obtain unlabelled data than labelled data. Semi-supervised learning is a bootstrapping method which incorporates a large amount of unlabelled data to improve the performance of supervised learning methods which lack sufficient labelled data.

Much of the semi-supervised learning in Computational Linguistics uses the iterative bootstrapping approach, initially proposed by Riloff and Shepherd [49] for building semantic lexicons, which later evolved into the learning of multiple categories [50]. These methods have further transformed to the semi-supervised learning of multiple related categories and relations as a method to enhance the learning process [51].

Instead of using this category of semi-supervised learning, we use a methodology called self-training. Ng and Cardie [52] proposed this type of semi-supervised learning to combat semantic drift [53, 54], a problem with the bootstrapped learning of multiple categories. They used bagging and majority voting in their implementation. A set of classifiers get trained on the labelled data, then they classify the unlabelled data independently. Only those predictions which have the same label by all classifiers are added to the training set and the classifiers are trained again. This process continues until a stop condition is met. For Clark et al. [55] a model is simply retrained at each iteration on its labelled data which is augmented with unlabelled data that is classified with the previous iteration’s model. According to this second method, there is only one classifier which is trained on labelled data. Then the resulting model is used to classify the unlabelled data. The most confident predictions are added to the training set and the classifier is retrained on this new training set. This procedure repeats for several rounds. We adopt this latter methodology in our work.

Rule-based and machine learning-based named entity relationship identification tools

Ibn Faiz [48] proposed a general-purpose software tool for mining relationships between named entities designed to be used in both a rule-based and a machine learning-based configuration. This tool was originally tailored to recognize pairs of interacting proteins and has been reconfigured here for the purpose of identifying genotype-phenotype relationships. Ibn Faiz [48] extended the rule-based method of RelEx [10] for identifying protein-protein interactions. In this method the dependency tree of each sentence is traversed according to some rules and various candidate dependency paths are extracted.

In addition to the linguistic patterns this method requires a good set of relationship terms. To find protein-protein interaction relationships, a list of interaction terms (a combination of lists from RelEx [10] and Bui et al. [11]) was used by Ibn Faiz to elicit protein-protein interactions. In the work reported below an appropriate set of relationship terms for genotype-phenotype relationships has been developed and used in the rule-based system to recognize this type of relationship.

Ibn Faiz [48] also used his general-purpose tool in a machine learning approach using a maximum entropy classifier and a set of relationship terms appropriate for identifying protein-protein interactions. This approach considers the relationship identification problem as a binary classification task. The Stanford dependency parser produces a dependency tree for each sentence. For each pair of named entities in a sentence, proteins in this case, the dependency path between them, the parse tree of the sentence, and other features are extracted. These features include: dependency features coming from the dependency representation of each sentence, syntactic features, and surface features derived directly from the raw text (the relationship terms and their relative position).

The extracted features along with the existence of a relationship between named entity pairs in a sentence make a feature vector. A machine learning model is trained based on the positive (a relationship exists) and negative (a relationship does not exist) examples. To avoid sparsity and overfitting problems, feature selection is used. Because the maximum entropy classifier and the linguistic dependency and syntactic features are the common foundation for this technique, only an appropriate set of relationship terms need to be provided for genotype-phenotype relationship identification. In the work reported below, the same set of relationship terms as used in the rule-based approach are used in the machine-learning approach.

Training set

At the beginning of the project we did not have any labelled data. Instead of using annotators knowledgeable in biomedicine to label a sufficiently large corpus of biomedical literature, we decided instead to use the previously described relationship identification tools modified to work with our data and use their agreed upon outputs, cleaned by a non-expert, as our labelled training set. This methodology has allowed us to partially evaluate this method of semi-automatic annotation.

As mentioned previously, the rule-based and machine learning-based systems for identifying biomedical relationships have been appropriately tailored to this task by supplying a set of genotype-phenotype relationship words that are appropriate for identifying this type of biomedical relationship. This set of relationship words includes a list of 20 verbs and two prepositions (in and for) from Rindflesch et al. [9] which encode a relationship between a genetic phenomenon and a disorder and the PPI relationship terms from Ibn Faiz’s work [48] which we found to apply also to genotype-phenotype relationships.²

After making corrections (see issues 2 and 4) and deleting sentences exhibiting issues 1 and 3, 430 sentences remained in the training set. These corrections and deletions were made by the first author. To increase the training set size, 39 additional sentences have been labelled manually and have been added to the training set. The data set is skewed: there are few negative instances. To address this imbalance, 40 sentences without any relationships have been selected manually and have been added to the training set. As shown in Table 3, the final training set has 509 sentences. There are 576 positive instances and 269 negative instances.

Test set

To ensure that the training set and the test set are independent, the test set is chosen from the initial set with the training set sentences removed. To select the sentences to be included in the test set, the results from processing our initial set with the two general purpose relationship identification tools have been used. In some cases both tools identify relationships from the same sentence but the relationships differ. For example in sentence “Common esr1 gene alleles-4 are unlikely to contribute to obesity-10 in women, whereas a minor importance of esr2-19 on obesity-21 cannot be excluded.” the machine learning-based tool finds a relationship between esr2-19 and obesity-21 but the rule-based tool claims that there is also a relationship between esr1 gene alleles-4 and obesity-10. Since we were confident that this type of sentence would provide a rich set of positive and negative instances, this type of sentence is extracted to make our initial test set of 298 sentences.

In order for the test set to provide a reasonable evaluation of the trained model, the sentences must be correctly labelled. A biochemistry graduate student was hired to annotate the initial test set. Pairs of genotypes and phenotypes are extracted from each sentence and her task was to indicate whether there is any relationship between them.

Issues 1 and 3 discussed in the previous section have been observed by the annotator in some of the sentences. Also, there are some cases where she is not sure if there is a relationship or not. Furthermore, she disagreed with the phenotypes and genotypes annotated in 54 sentences. After deleting these 54 problematic sentences the final test set comprises 244 sentences (which contain 536 positive instances and 287 negative instances). See Table 3.

Unlabelled data

After choosing the training and testing sentences from the initial set of sentences, the remaining sentences have been used as unlabelled data. The unlabelled set contains 3440 sentences. A subset of these (408 sentences containing 823 instances which approximates the number found in the original training set) are used in the self-training step⁴.

Self-training algorithm

The first model is trained using the training set and the machine learning method described earlier. To improve the performance of our model, a self-training process has been applied. Figure 3 outlines this process. This process starts with the provided labelled data and unlabelled data. The labelled data is used to train a model which is used to tag the unlabelled data. In most self-training algorithms the instances with the highest confidence level are selected to be added to the labelled data. However, as has been observed in some self-training algorithms, choosing the most confident unlabelled instances and adding them to the labelled data can cause overfitting [60]. We encountered a similar overfitting when we added the most confident unlabelled instances. So we considered the following two measures to select the best unlabelled instances.

• The confidence level must be in an interval. It must be more than a threshold α and less than a specified value β.

• The predicted value of the selected instances must be the same as their predicted value by the rule-based system.

In each iteration an at most upper-bounded number of instances are selected and added to the labelled data to prevent adding lots of incorrectly labelled data to the training set in the first iterations when the model is not powerful enough to make good predictions.

We used relationship identification output from the PPI-tailored rule-based tool as an added level of conservatism in the decision to add an unlabelled instance to the training set. It has only moderate performance on genotype-phenotype relationship identification. So, using this tool’s advice along with the confidence level means that the relationship must be of a more general nature than just genotype-phenotype relationships. However, at some point this conservatism holds the system back from learning broader types of relationships in the genotype-phenotype category. Therefore this selection factor is used only for the first i iterations, and after i iterations the best unlabelled data is chosen based only on the confidence level. Again, here, the confidence level must be in an interval.

This proposed self-training algorithm has been tried with various configurations and each variable in this process has been given several values. Each resulting model has been tried separately with our test set and the best system is selected based on its performance on the test set. In our best configuration 15 unlabelled instances are added to the labelled data in each iteration, in the first 5 iterations predictions made by the rule-based system are taken into account, the least confidence level is 85%, the highest confidence level is 92% and the process stops after 6 iterations.