A Simple Standard for Sharing Ontological Mappings (SSSOM)

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases

Geospatial crowdsourced data fitness analysis for spatial data infrastructure based disaster management actions

The reporting of disasters has changed from official media reports to citizen reporters who are at the disaster scene. This kind of crowd based reporting, related to disasters or any other events, is often identified as 'Crowdsourced Data' (CSD). CSD are freely and widely available thanks to the current technological advancements. The quality of CSD is often problematic as it is often created by the citizens of varying skills and backgrounds. CSD is considered unstructured in general, and its quality remains poorly defined. Moreover, the CSD's location availability and the quality of any available locations may be incomplete. The traditional data quality assessment methods and parameters are also often incompatible with the unstructured nature of CSD due to its undocumented nature and missing metadata. Although other research has identified credibility and relevance as possible CSD quality assessment indicators, the available assessment methods for these indicators are still immature. In the 2011 Australian floods, the citizens and disaster management administrators used the Ushahidi Crowd-mapping platform and the Twitter social media platform to extensively communicate flood related information including hazards, evacuations, help services, road closures and property damage. This research designed a CSD quality assessment framework and tested the quality of the 2011 Australian floods' Ushahidi Crowdmap and Twitter data. In particular, it explored a number of aspects namely, location availability and location quality assessment, semantic extraction of hidden location toponyms and the analysis of the credibility and relevance of reports. This research was conducted based on a Design Science (DS) research method which is often utilised in Information Science (IS) based research. Location availability of the Ushahidi Crowdmap and the Twitter data assessed the quality of available locations by comparing three different datasets i.e. Google Maps, OpenStreetMap (OSM) and Queensland Department of Natural Resources and Mines' (QDNRM) road data. Missing locations were semantically extracted using Natural Language Processing (NLP) and gazetteer lookup techniques. The Credibility of Ushahidi Crowdmap dataset was assessed using a naive Bayesian Network (BN) model commonly utilised in spam email detection. CSD relevance was assessed by adapting Geographic Information Retrieval (GIR) relevance assessment techniques which are also utilised in the IT sector. Thematic and geographic relevance were assessed using Term Frequency – Inverse Document Frequency Vector Space Model (TF-IDF VSM) and NLP based on semantic gazetteers. Results of the CSD location comparison showed that the combined use of non-authoritative and authoritative data improved location determination. The semantic location analysis results indicated some improvements of the location availability of the tweets and Crowdmap data; however, the quality of new locations was still uncertain. The results of the credibility analysis revealed that the spam email detection approaches are feasible for CSD credibility detection. However, it was critical to train the model in a controlled environment using structured training including modified training samples. The use of GIR techniques for CSD relevance analysis provided promising results. A separate relevance ranked list of the same CSD data was prepared through manual analysis. The results revealed that the two lists generally agreed which indicated the system's potential to analyse relevance in a similar way to humans. This research showed that the CSD fitness analysis can potentially improve the accuracy, reliability and currency of CSD and may be utilised to fill information gaps available in authoritative sources. The integrated and autonomous CSD qualification framework presented provides a guide for flood disaster first responders and could be adapted to support other forms of emergencies

Generation and Applications of Knowledge Graphs in Systems and Networks Biology

The acceleration in the generation of data in the biomedical domain has necessitated the use of computational approaches to assist in its interpretation. However, these approaches rely on the availability of high quality, structured, formalized biomedical knowledge. This thesis has the two goals to improve methods for curation and semantic data integration to generate high granularity biological knowledge graphs and to develop novel methods for using prior biological knowledge to propose new biological hypotheses. The first two publications describe an ecosystem for handling biological knowledge graphs encoded in the Biological Expression Language throughout the stages of curation, visualization, and analysis. Further, the second two publications describe the reproducible acquisition and integration of high-granularity knowledge with low contextual specificity from structured biological data sources on a massive scale and support the semi-automated curation of new content at high speed and precision. After building the ecosystem and acquiring content, the last three publications in this thesis demonstrate three different applications of biological knowledge graphs in modeling and simulation. The first demonstrates the use of agent-based modeling for simulation of neurodegenerative disease biomarker trajectories using biological knowledge graphs as priors. The second applies network representation learning to prioritize nodes in biological knowledge graphs based on corresponding experimental measurements to identify novel targets. Finally, the third uses biological knowledge graphs and develops algorithmics to deconvolute the mechanism of action of drugs, that could also serve to identify drug repositioning candidates. Ultimately, the this thesis lays the groundwork for production-level applications of drug repositioning algorithms and other knowledge-driven approaches to analyzing biomedical experiments

On Elemental Phenomenology: Sallis and Dzogchen Buddhism

John Sallis’ volumes on the Force of the Imagination (2000) and Logic of the Imagination (2012) constitute, in the field of contemporary Continental thought, a novel philosophical view of the elementals. Tibetan Buddhism has a more than a thousand-year old tradition of teaching about and practicing with the elements. This study is a preliminary exploration of the cross-currents of these two elemental teachings