Alexander Garcia

• PhD
• Research Associate at Graz University of Technology

During the last decades, there has been significant changes in science that have provoked a big increase in the number of articles published every year. This increment implies a new difficulty for scientists, who have to do an extra effort for selecting literature relevant for their activity. In this work, we present a pipeline for the generation o...

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results. Bioschemas is based on th...

Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements. This article presents a guideline for describing key content for reporting experimental protocols in the...

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the se...

using blockchain for preserving the research life cycle

Using Blockchain in order to preserve the digital life cycle

With the continuous creation, sharing and transformation of data resulting from Research and Development in the Life Sciences domain, provenance tracking and valorization of research outputs remain challenges. Tracing biomed-ical materials and associated data throughout the research life cycle requires tracking materials, methods, transformations,...

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the se...

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the se...

Background An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other...

10.6084/m9.figshare.5259919.v1 also available at https://figshare.com/articles/Thinking_of_a_Blockchain_for_VIVO/5259919 VIVO is an example of a decentralized system; institutions publish VIVO data just by adhering to a simple data structure in the form of an ontology. Similar to a distributed ledger, VIVO is a decentralized database that is used t...

Robotic Crowd Biology: LabDroids accelerate life science experiments

In this paper we present the Semantic Enhancement for the Open Journal Systems, SE4OJS, to generate semantically annotated documents. With this tool, we created a knowl-edgebase for psychology, KOBPSY. We have identified structural document elements such as authors, sections, and domain knowledge about diseases, population, treatments and more. Our...

Motivation: Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text ba...

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source so...

In this paper we propose an automatic method for building domain ontologies where we leverage the emerging vocabulary from social tagging systems, and the existing semantics in the Linked Open Data cloud to enrich semantically the terms that shape the domain ontology. We systematically capture a domain vocabulary by searching for relevant resources...

Two important characteristics of science are the "reproducibility" and "clarity". By rigorous practices, scientists explore aspects of the world that they can reproduce under carefully controlled experimental conditions. The clarity, complementing reproducibility, provides unambiguous descriptions of results in a mechanical or mathematical form. Bo...

We describe a domain ontology development approach that extracts domain terms from folksonomies and enrich them with data and vocabularies from the Linked Open Data cloud. As a result, we obtain lightweight domain ontologies that combine the emergent knowledge of social tagging systems with formal knowledge from Ontologies. In order to illustrate t...

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionalit...

SePublica 2013 Semantic Publishing Proceedings of the 3rd Workshop on Semantic Publishing Montpellier, France, May 26th, 2013. Edited by Alexander García Castro, Florida State University, USA Christoph Lange, University of Birmingham, UK Phillip Lord, Newcastle University, UK Robert Stevens, University of Manchester, UK

The core information from scientific publications is encoded in natural language text and monolithic documents; therefore it is not well integrated with other structured and unstructured data resources. The text format requires additional processing to semantically interlink the publications and to finally reach interoperability of contained data....

Availability: http://www.jbiomedsem.com/content/4/S1/S5 Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology...

BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configura...

Nowadays one of the biggest problems many manufacturing companies face is the loss of knowledge from the information it possesses. Whether it tries to make business or improves the exchange of information within its different areas, valuable knowledge does not reach all stakeholders due to abstraction and ambiguity. A clear example in which both pr...

SePublica 2012 Semantic Publishing Proceedings of the 2nd Workshop on Semantic Publishing Hersonissos, Crete, Greece, May 28th, 2012. Edited by Alexander García Castro, Florida State University, USA Christoph Lange, University of Birmingham, UK Frank van Harmelen, Vrije Universiteit Amsterdam, Netherlands Benjamin Good, Scripps Research Institut...

In this paper, we introduce the approach we are taking to generate a knowledge model for biomedical literature with the ultimate goal of improving information retrieval over our digital library and facilitating the discovery of hidden relationships across papers. Existing ontologies are brought together in order to facilitate the representation of...

We have reviewed different approaches on community-based annotation on protein and gene sequences, mainly relying on the wiki paradigms. Currently such approaches are not fully exploiting the social component that naturally emerges within communities. We propose a model, namely Tagsty, that enables a community to semantically annotate protein seque...

Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previou...

SePublica-2011 Semantic Publishing 2011 Proceedings of the 1st Workshop on Semantic Publishing 2011 co-located with the 8th Extended Semantic Web Conference, ESWC2011 Hersonissos, Crete, Greece, May 30, 2011.

DAS GFF Example. Example of a file that follows the DAS GFF format and can be used as input for the writeback server.

Usability report. This is list of the findings of the usability experiment for the writeback extension on Dasty.

Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environ...

The Hyperontology framework has been recently introduced to provide a general methodology for heterogeneous ontology design, i.e. the construction of ontologies that have parts, or modules, written in different formalisms, and which are interlinked in complex ways. We here present a brief outline of this framework, discuss its features and merits,...

This paper describes the design and implementation of an Ontology- Based System for Features Recognition and Design Rules Checking in the domain of sheet-metal engineering using Semantic Web technologies. The system was implemented by means of the Protégé Application Programming Interface (API), a rule engine and a reasoner. Using ontology in the c...

In this position paper we analyze the similarities amongst folksonomies, semantic wikis, and ontology building; we also propose an alignment and orchestration of ontologies representing these scenarios. We argue that such alignment enables a more direct application of folksonomybased approaches over these set-ups. The rationale behind folksonomies...

We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of...

We briefly describe the methodology we have adopted in order to develop ontologies. Because our scenarios involved domain experts distributed geographically, the domain analysis and knowledge acquisition phases used different independent technologies that were not always integrated into the Protégé suite. Groupware capabilities were thus achieved....

The use of ontologies to facilitate semantic annotation of medical images has been a widely used approach. A particular limitation of this approach is the lack of ontologies with a high level of completeness, mainly because the problem that ontology evolution represent. This article proposes an approach that facilitates the evolution of ontologies...

Social Tagging Systems (STS) empower users to classify and organize resources and to improve the retrieval performance over the tagged resources. In this paper we argue that the potential of the social process of assigning, finding, and relating symbols in collaborative tagging scenarios is currently underexploited and can be increased by extending...

This chapter addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This chap...

Rather than a document that is constantly being written as in the wiki approach, the Living Document (LD) is a document that also acts as a document router, operating by means of structured and organized social tagging and using existing ontologies. It offers an environment where users can manage papers and related information, share their knowledg...

Tagging has become,increasingly popular and useful across various social networks,and,applications. It allows,users to classify and,organize resources for improving,the retrieval performance,over those tagged resources. Within social networks, tags can also facilitate the interaction between members of the community, e.g. because similar tags may r...

Rather than a document that is being constantly re-written as in the wiki approach, the Living Document (LD) is one that acts as a document router, operating by means of structured and organized social tagging and existing ontologies. It offers an environment where users can manage papers and related information, share their knowledge with their pe...

Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at th...

Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at th...

This paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper...

This paper presents OLS2OWL, an ontology repository manager plug-in developed for Protégé 4.0. The tool (1) facilitates search and retrieval over collections of ontologies, (2) supports comparison across terms from different ontologies by providing integrative views; the latter supports weaving and maintaining a dense network of semantic relationsh...

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by...

Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS). Availability: Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.

This paper discusses the design challenges encountered when building an ontology repository for an application framework devoted to assistive technologies that can be browsed and queried in a highly heterogeneous and expressive way. As a main vehicle to achieve this goal we propose to use metadata and meta-reasoning. We analyze how metadata can be...

This paper presents a framework for the semantic alignment of Web services within the context of ASK-IT project. This alignment heavily relies on ontologies. The main aim of the presented framework is to enable different service providers to map their Web services against a common ontological framework in order to support the discovery and invocati...

In this paper, we present MAP2OWL, a software tool that allows the development of OWL ontologies as concept maps. MAP2OWL uses existing OWL constructs to represent conceptual maps; in this way, domain experts develop ontolologies in a graphical conceptual way, not having to be aware of syntactic matters, or issues related to interfaces that were de...

With the explosion of biological data in the postgenomic era, there has been a growing need for semantic data integration, supported by ontologies. Semantic integration techniques enable biologists to construct complex biological queries. However, the construction of these queries and analysis of their results can place a high cognitive load on bio...

Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standar...

Integrating information in the molecular biosciences involves more than the cross-referencing of sequences or structures. Experimental protocols, results of computational analyses, annotations and links to relevant literature form integral parts of this information, and impart meaning to sequence or structure. In this review, we examine some existi...

Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics,...

Tecnología Open-source para aplicaciones en la bioquímica y la biología molecular.

ABSTRACT: Trauma patients present a hypercoagulable state that predisposes to thromboembolism. Tissue plasminogen activator (t-PA), plasminogen activator inhibitor (PAI), plasminogen, α2-antiplasmin, D-D dimer fibrin fragments, protein C, protein S, antithrombin III (AT-III), fibrinogen, factor II Ag, Von Willebrand factor related antigen (VWF:Ag),...

As in software engineering, documentation is crucial for engi-neering reliable ontologies. Despite improvements in OWL 2, documen-tation inside ontologies still has shortcomings. We take the approach of embedding OWL ontologies into the host language OMDoc – a language for representing mathematical knowledge in a wide range of expressivity and with...

Motivation: The Web has succeeded as a dissemination platform for scientific and non-scientific papers, news, and communication in general; however, most of that information remains locked up in discrete documents, which are poorly interconnected to one another and to the Web itself. The connectivity tissue provided by RDF technology and the So-cia...

The development of &quot omic&quot technologies and its applications into biological sciences has increased the need for an integrated view of bio-related information. The flood of information as well as the technological availability has made it necessary for researchers to share resources and join efforts more than ever in order to understand the...

Structuring and supporting the argumentative process that takes place within the knowledge elicitation process is a major problem when developing ontologies. Knowledge elicitation relies heavily on the argumentative process amongst domain experts. The involvement of geographically distributed domain experts and the need for domain experts to lead t...

The current science landscape is rapidly evolving and it is increasingly driven by computational tasks. The deluge of data unleashed by omics-technologies, such as transcriptomics, proteomics and metabolomics, requires systematic approaches for reporting and storing the data and the experimental processes in a standard format, relating the biology...

In this paper we describe a two-step approach for the publication of data about displaced people in Colombia, whose lack of homogeneity represents a major barrier for the application of adequate policies. This data is available in heterogeneous data sources, mainly relational, and is not connected to social networking sites. Our approach consists i...