NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

Improving Code Example Recommendations on Informal Documentation Using BERT and Query-Aware LSH: A Comparative Study

Our research investigates the recommendation of code examples to aid software developers, a practice that saves developers significant time by providing ready-to-use code snippets. The focus of our study is Stack Overflow, a commonly used resource for coding discussions and solutions, particularly in the context of the Java programming language. We applied BERT, a powerful Large Language Model (LLM) that enables us to transform code examples into numerical vectors by extracting their semantic information. Once these numerical representations are prepared, we identify Approximate Nearest Neighbors (ANN) using Locality-Sensitive Hashing (LSH). Our research employed two variants of LSH: Random Hyperplane-based LSH and Query-Aware LSH. We rigorously compared these two approaches across four parameters: HitRate, Mean Reciprocal Rank (MRR), Average Execution Time, and Relevance. Our study revealed that the Query-Aware (QA) approach showed superior performance over the Random Hyperplane-based (RH) method. Specifically, it exhibited a notable improvement of 20% to 35% in HitRate for query pairs compared to the RH approach. Furthermore, the QA approach proved significantly more time-efficient, with its speed in creating hashing tables and assigning data samples to buckets being at least four times faster. It can return code examples within milliseconds, whereas the RH approach typically requires several seconds to recommend code examples. Due to the superior performance of the QA approach, we tested it against PostFinder and FaCoY, the state-of-the-art baselines. Our QA method showed comparable efficiency proving its potential for effective code recommendation

On Using Machine Learning to Identify Knowledge in API Reference Documentation

Using API reference documentation like JavaDoc is an integral part of software development. Previous research introduced a grounded taxonomy that organizes API documentation knowledge in 12 types, including knowledge about the Functionality, Structure, and Quality of an API. We study how well modern text classification approaches can automatically identify documentation containing specific knowledge types. We compared conventional machine learning (k-NN and SVM) and deep learning approaches trained on manually annotated Java and .NET API documentation (n = 5,574). When classifying the knowledge types individually (i.e., multiple binary classifiers) the best AUPRC was up to 87%. The deep learning and SVM classifiers seem complementary. For four knowledge types (Concept, Control, Pattern, and Non-Information), SVM clearly outperforms deep learning which, on the other hand, is more accurate for identifying the remaining types. When considering multiple knowledge types at once (i.e., multi-label classification) deep learning outperforms na\"ive baselines and traditional machine learning achieving a MacroAUC up to 79%. We also compared classifiers using embeddings pre-trained on generic text corpora and StackOverflow but did not observe significant improvements. Finally, to assess the generalizability of the classifiers, we re-tested them on a different, unseen Python documentation dataset. Classifiers for Functionality, Concept, Purpose, Pattern, and Directive seem to generalize from Java and .NET to Python documentation. The accuracy related to the remaining types seems API-specific. We discuss our results and how they inform the development of tools for supporting developers sharing and accessing API knowledge. Published article: https://doi.org/10.1145/3338906.333894

A Decade of Code Comment Quality Assessment: A Systematic Literature Review

Code comments are important artifacts in software systems and play a paramount role in many software engineering (SE) tasks related to maintenance and program comprehension. However, while it is widely accepted that high quality matters in code comments just as it matters in source code, assessing comment quality in practice is still an open problem. First and foremost, there is no unique definition of quality when it comes to evaluating code comments. The few existing studies on this topic rather focus on specific attributes of quality that can be easily quantified and measured. Existing techniques and corresponding tools may also focus on comments bound to a specific programming language, and may only deal with comments with specific scopes and clear goals (e.g., Javadoc comments at the method level, or in-body comments describing TODOs to be addressed). In this paper, we present a Systematic Literature Review (SLR) of the last decade of research in SE to answer the following research questions: (i) What types of comments do researchers focus on when assessing comment quality? (ii) What quality attributes (QAs) do they consider? (iii) Which tools and techniques do they use to assess comment quality?, and (iv) How do they evaluate their studies on comment quality assessment in general? Our evaluation, based on the analysis of 2353 papers and the actual review of 47 relevant ones, shows that (i) most studies and techniques focus on comments in Java code, thus may not be generalizable to other languages, and (ii) the analyzed studies focus on four main QAs of a total of 21 QAs identified in the literature, with a clear predominance of checking consistency between comments and the code. We observe that researchers rely on manual assessment and specific heuristics rather than the automated assessment of the comment quality attributes