Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts

Many of the most commonly explored natural language processing (NLP) information extraction tasks can be thought of as evaluations of declarative knowledge, or fact-based information extraction. Procedural knowledge extraction, i.e., breaking down a described process into a series of steps, has received much less attention, perhaps in part due to the lack of structured datasets that capture the knowledge extraction process from end-to-end. To address this unmet need, we present FlaMB\'e (Flow annotations for Multiverse Biological entities), a collection of expert-curated datasets across a series of complementary tasks that capture procedural knowledge in biomedical texts. This dataset is inspired by the observation that one ubiquitous source of procedural knowledge that is described as unstructured text is within academic papers describing their methodology. The workflows annotated in FlaMB\'e are from texts in the burgeoning field of single cell research, a research area that has become notorious for the number of software tools and complexity of workflows used. Additionally, FlaMB\'e provides, to our knowledge, the largest manually curated named entity recognition (NER) and disambiguation (NED) datasets for tissue/cell type, a fundamental biological entity that is critical for knowledge extraction in the biomedical research domain. Beyond providing a valuable dataset to enable further development of NLP models for procedural knowledge extraction, automating the process of workflow mining also has important implications for advancing reproducibility in biomedical research.Comment: Submitted to NeurIPS 2023 Datasets and Benchmarks Trac

Bridging the gap between textual and formal business process representations

Tesi en modalitat de compendi de publicacionsIn the era of digital transformation, an increasing number of organizations are start ing to think in terms of business processes. Processes are at the very heart of each business, and must be understood and carried out by a wide range of actors, from both technical and non-technical backgrounds alike. When embracing digital transformation practices, there is a need for all involved parties to be aware of the underlying business processes in an organization. However, the representational complexity and biases of the state-of-the-art modeling notations pose a challenge in understandability. On the other hand, plain language representations, accessible by nature and easily understood by everyone, are often frowned upon by technical specialists due to their ambiguity. The aim of this thesis is precisely to bridge this gap: Between the world of the techni cal, formal languages and the world of simpler, accessible natural languages. Structured as an article compendium, in this thesis we present four main contributions to address specific problems in the intersection between the fields of natural language processing and business process management.A l’era de la transformació digital, cada vegada més organitzacions comencen a pensar en termes de processos de negoci. Els processos són el nucli principal de tota empresa i, com a tals, han de ser fàcilment comprensibles per un ampli ventall de rols, tant perfils tècnics com no-tècnics. Quan s’adopta la transformació digital, és necessari que totes les parts involucrades estiguin ben informades sobre els protocols implantats com a part del procés de digitalització. Tot i això, la complexitat i biaixos de representació dels llenguatges de modelització que actualment conformen l’estat de l’art sovint en dificulten la seva com prensió. D’altra banda, les representacions basades en documentació usant llenguatge natural, accessibles per naturalesa i fàcilment comprensibles per tothom, moltes vegades són vistes com un problema pels perfils més tècnics a causa de la presència d’ambigüitats en els textos. L’objectiu d’aquesta tesi és precisament el de superar aquesta distància: La distància entre el món dels llenguatges tècnics i formals amb el dels llenguatges naturals, més accessibles i senzills. Amb una estructura de compendi d’articles, en aquesta tesi presentem quatre grans línies de recerca per adreçar problemes específics en aquesta intersecció entre les tecnologies d’anàlisi de llenguatge natural i la gestió dels processos de negoci.Postprint (published version

Systematising and scaling literature curation for genetically determined developmental disorders

The widespread availability of genomic sequencing has transformed the diagnosis of genetically-determined developmental disorders (GDD). However, this type of test often generates a number of genetic variants, which have to be reviewed and related back to the clinical features (phenotype) of the individual being tested. This frequently entails a time-consuming review of the peer-reviewed literature to look for case reports describing variants in the gene(s) of interest. This is particularly true for newly described and/or very rare disorders not covered in phenotype databases. Therefore, there is a need for scalable, automated literature curation to increase the efficiency of this process. This should lead to improvements in the speed in which diagnosis is made, and an increase in the number of individuals who are diagnosed through genomic testing. Phenotypic data in case reports/case series is not usually recorded in a standardised, computationally-tractable format. Plain text descriptions of similar clinical features may be recorded in several different ways. For example, a technical term such as ‘hypertelorism’, may be recorded as its synonym ‘widely spaced eyes’. In addition, case reports are found across a wide range of journals, with different structures and file formats for each publication. The Human Phenotype Ontology (HPO) was developed to store phenotypic data in a computationally-accessible format. Several initiatives have been developed to link diseases to phenotype data, in the form of HPO terms. However, these rely on manual expert curation and therefore are not inherently scalable, and cannot be updated automatically. Methods of extracting phenotype data from text at scale developed to date have relied on abstracts or open access papers. At the time of writing, Europe PubMed Central (EPMC, https://europepmc.org/) contained approximately 39.5 million articles, of which only 3.8 million were open access. Therefore, there is likely a significant volume of phenotypic data which has not been used previously at scale, due to difficulties accessing non-open access manuscripts. In this thesis, I present a method for literature curation which can utilise all relevant published full text through a newly developed package which can download almost all manuscripts licenced by a university or other institution. This is scalable to the full spectrum of GDD. Using manuscripts identified through manual literature review, I use a full text download pipeline and NLP (natural language processing) based methods to generate disease models. These are comprised of HPO terms weighted according to their frequency in the literature. I demonstrate iterative refinement of these models, and use a custom annotated corpus of 50 papers to show the text mining process has high precision and recall. I demonstrate that these models clinically reflect true disease expressivity, as defined by manual comparison with expert literature reviews, for three well-characterised GDD. I compare these disease models to those in the most commonly used genetic disease phenotype databases. I show that the automated disease models have increased depth of phenotyping, i.e. there are more terms than those which are manually-generated. I show that, in comparison to ‘real life’ prospectively gathered phenotypic data, automated disease models outperform existing phenotype databases in predicting diagnosis, as defined by increased area under the curve (by 0.05 and 0.08 using different similarity measures) on ROC curve plots. I present a method for automated PubMed search at scale, to use as input for disease model generation. I annotated a corpus of 6500 abstracts. Using this corpus I show a high precision (up to 0.80) and recall (up to 1.00) for machine learning classifiers used to identify manuscripts relevant to GDD. These use hand-picked domain-specific features, for example utilising specific MeSH terms. This method can be used to scale automated literature curation to the full spectrum of GDD. I also present an analysis of the phenotypic terms used in one year of GDD-relevant papers in a prominent journal. This shows that use of supplemental data and parsing clinical report sections from manuscripts is likely to result in more patient-specific phenotype extraction in future. In summary, I present a method for automated curation of full text from the peer-reviewed literature in the context of GDD. I demonstrate that this method is robust, reflects clinical disease expressivity, outperforms existing manual literature curation, and is scalable. Applying this process to clinical testing in future should improve the efficiency and accuracy of diagnosis

Text Mining for Chemical Compounds

Exploring the chemical and biological space covered by patent and journal publications is crucial in early- stage medicinal chemistry activities. The analysis provides understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents and journals through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. In this book, we addressed the lack of quality measurements for assessing the correctness of structural representation within and across chemical databases; lack of resources to build text-mining systems; lack of high performance systems to extract chemical compounds from journals and patents; and lack of automated systems to identify relevant compounds in patents. The consistency and ambiguity of chemical identifiers was analyzed within and between small- molecule databases in Chapter 2 and Chapter 3. In Chapter 4 and Chapter 7 we developed resources to enable the construction of chemical text-mining systems. In Chapter 5 and Chapter 6, we used community challenges (BioCreative V and BioCreative VI) and their corresponding resources to identify mentions of chemical compounds in journal abstracts and patents. In Chapter 7 we used our findings in previous chapters to extract chemical named entities from patent full text and to classify the relevancy of chemical compounds

Plagiarism detection for Indonesian texts

As plagiarism becomes an increasing concern for Indonesian universities and research centers, the need of using automatic plagiarism checker is becoming more real. However, researches on Plagiarism Detection Systems (PDS) in Indonesian documents have not been well developed, since most of them deal with detecting duplicate or near-duplicate documents, have not addressed the problem of retrieving source documents, or show tendency to measure document similarity globally. Therefore, systems resulted from these researches are incapable of referring to exact locations of ``similar passage'' pairs. Besides, there has been no public and standard corpora available to evaluate PDS in Indonesian texts. To address the weaknesses of former researches, this thesis develops a plagiarism detection system which executes various methods of plagiarism detection stages in a workflow system. In retrieval stage, a novel document feature coined as phraseword is introduced and executed along with word unigram and character n-grams to address the problem of retrieving source documents, whose contents are copied partially or obfuscated in a suspicious document. The detection stage, which exploits a two-step paragraph-based comparison, is aimed to address the problems of detecting and locating source-obfuscated passage pairs. The seeds for matching source-obfuscated passage pairs are based on locally-weighted significant terms to capture paraphrased and summarized passages. In addition to this system, an evaluation corpus was created through simulation by human writers, and by algorithmic random generation. Using this corpus, the performance evaluation of the proposed methods was performed in three scenarios. On the first scenario which evaluated source retrieval performance, some methods using phraseword and token features were able to achieve the optimum recall rate 1. On the second scenario which evaluated detection performance, our system was compared to Alvi's algorithm and evaluated in 4 levels of measures: character, passage, document, and cases. The experiment results showed that methods resulted from using token as seeds have higher scores than Alvi's algorithm in all 4 levels of measures both in artificial and simulated plagiarism cases. In case detection, our systems outperform Alvi's algorithm in recognizing copied, shaked, and paraphrased passages. However, Alvi's recognition rate on summarized passage is insignificantly higher than our system. The same tendency of experiment results were demonstrated on the third experiment scenario, only the precision rates of Alvi's algorithm in character and paragraph levels are higher than our system. The higher Plagdet scores produced by some methods in our system than Alvi's scores show that this study has fulfilled its objective in implementing a competitive state-of-the-art algorithm for detecting plagiarism in Indonesian texts. Being run at our test document corpus, Alvi's highest scores of recall, precision, Plagdet, and detection rate on no-plagiarism cases correspond to its scores when it was tested on PAN'14 corpus. Thus, this study has contributed in creating a standard evaluation corpus for assessing PDS for Indonesian documents. Besides, this study contributes in a source retrieval algorithm which introduces phrasewords as document features, and a paragraph-based text alignment algorithm which relies on two different strategies. One of them is to apply local-word weighting used in text summarization field to select seeds for both discriminating paragraph pair candidates and matching process. The proposed detection algorithm results in almost no multiple detection. This contributes to the strength of this algorithm

The classification of gene products in the molecular biology domain: Realism, objectivity, and the limitations of the Gene Ontology

Background: Controlled vocabularies in the molecular biology domain exist to facilitate data integration across database resources. One such tool is the Gene Ontology (GO), a classification designed to act as a universal index for gene products from any species. The Gene Ontology is used extensively in annotating gene products and analysing gene expression data, yet very little research exists from a library and information science perspective exploring the design principles, philosophy and social role of ontologies in biology. Aim: To explore how molecular biologists, in creating the Gene Ontology, devised guidelines and rules for determining which scientific concepts are included in the ontology, and the criteria for how these concepts are represented. Methods: A domain analysis approach was used to devise a mixed methodology to study the design of the Gene Ontology. Concept analysis of a GO term and a critical discourse analysis of GO developer mailing list texts were used to test whether ontological realism is a tenable basis for constructing objective ontologies. A comparison of the current GO vocabulary construction guidelines and a study of the reasons why GO terms are removed from the ontology further explored the justifications for the design of the Gene Ontology. Finally, a content analysis of published GO papers examined how authors use and cite GO data and terminology. Results: Gene Ontology terms can be presented according to different epistemologies for concepts, indicating that ontological realism is not the only way objective ontologies can be designed. Social roles and the exercise of power were found to play an important role in determining ontology content, and poor synonym control, a lack of clear warrant for deciding terminology and arbitrary decisions to delete and invent new terms undermine the objectivity and universal applicability of the Gene Ontology. Authors exhibited poor compliance with GO data citation policies, and in re-wording and misquoting GO terminology, risk exacerbating the semantic problems this controlled vocabulary was designed to solve. Conclusions: The failure of the Gene Ontology to define what is meant by a molecular function, the exercise of power by GO developers in clearing contentious concepts from the ontology, and the strict adherence to ontological realism, which marginalises social and subjective ways of classifying scientific concepts, limits the utility of the ontology as a tool to unify the molecular biology domain. These limitations to the Gene Ontology design could be overcome with the development of lighter, pluralistic, user-controlled ‘open ontologies’ for gene products that can work alongside more traditional, ‘top-down’ developed vocabularies

Modeling Faceted Browsing with Category Theory for Reuse and Interoperability

Faceted browsing (also called faceted search or faceted navigation) is an exploratory search model where facets assist in the interactive navigation of search results. Facets are attributes that have been assigned to describe resources being explored; a faceted taxonomy is a collection of facets provided by the interface and is often organized as sets, hierarchies, or graphs. Faceted browsing has become ubiquitous with modern digital libraries and online search engines, yet the process is still difficult to abstractly model in a manner that supports the development of interoperable and reusable interfaces. We propose category theory as a theoretical foundation for faceted browsing and demonstrate how the interactive process can be mathematically abstracted in order to support the development of reusable and interoperable faceted systems. Existing efforts in facet modeling are based upon set theory, formal concept analysis, and light-weight ontologies, but in many regards they are implementations of faceted browsing rather than a specification of the basic, underlying structures and interactions. We will demonstrate that category theory allows us to specify faceted objects and study the relationships and interactions within a faceted browsing system. Resulting implementations can then be constructed through a category-theoretic lens using these models, allowing abstract comparison and communication that naturally support interoperability and reuse. In this context, reuse and interoperability are at two levels: between discrete systems and within a single system. Our model works at both levels by leveraging category theory as a common language for representation and computation. We will establish facets and faceted taxonomies as categories and will demonstrate how the computational elements of category theory, including products, merges, pushouts, and pullbacks, extend the usefulness of our model. More specifically, we demonstrate that categorical constructions such as the pullback and pushout operations can help organize and reorganize facets; these operations in particular can produce faceted views containing relationships not found in the original source taxonomy. We show how our category-theoretic model of facets relates to database schemas and discuss how this relationship assists in implementing the abstractions presented. We give examples of interactive interfaces from the biomedical domain to help illustrate how our abstractions relate to real-world requirements while enabling systematic reuse and interoperability. We introduce DELVE (Document ExpLoration and Visualization Engine), our framework for developing interactive visualizations as modular Web-applications in order to assist researchers with exploratory literature search. We show how facets relate to and control visualizations; we give three examples of text visualizations that either contain or interact with facets. We show how each of these visualizations can be represented with our model and demonstrate how our model directly informs implementation. With our general framework for communicating consistently about facets at a high level of abstraction, we enable the construction of interoperable interfaces and enable the intelligent reuse of both existing and future efforts