Heidelberg, Baden-Württemberg, Germany
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Expert in Ontology Management Frameworks and Ontology Engineering, Knowledge Graphs, Data...

Articles by Alexander

  • On Reference Designation Systems and ISO/IEC 81346 as enablers of FAIR data
    Mar 23, 2025

    On Reference Designation Systems and ISO/IEC 81346 as enablers of FAIR data

    The Reference Designation System (RDS), defined in the ISO/IEC 81346 standard series, provides a method to identify...

    1 Comment
  • Notes from Cheers and Data
    Mar 26, 2024

    Notes from Cheers and Data

    Yesterday we had a very nice and vivid discussion about all things data. Thanks Sebastian Schmidt Pavel Klinov Mohammad...

    4 Comments
  • Why data is so difficult for companies?
    Jan 21, 2019

    Why data is so difficult for companies?

    I have seen many cases where companies find it difficult to define and implement a data strategy. Ontologies, Machine...

  • neo4j and triplet stores
    Nov 7, 2018

    neo4j and triplet stores

    neo4j vs triplet stores, is there a vs? I am looking at neo4j and I wonder what is it that neo4j does that a triplet...

    3 Comments
  • Connections across scientific publications
    Aug 10, 2015

    Connections across scientific publications

    Connections across scientific publications based on semantic annotations, check http://ceur-ws.org/Vol-994/paper-05.

Activity

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Experience & Education

  • Siemens Energy

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Volunteer Experience

  • Instrcutor

    ACCEFYN

    Science and Technology

    RasMol and Chime we well as other visualization tools

Publications

  • Conceptual Exploration of Documents and Digital Libraries in the Biomedical Domain

    SWAT4LS 2012 Paris, ISSN 1613-0073 Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences

    In this demo we present our approach to the use of Semantic Web technology in scholarly communications; it entails the understanding of re- search papers as an interface to the Web of Data. We are using the connectivity tissue provided by RDF technologies in order to facilitate semantic retrieval as well as to improve the user-experience when interacting with biomedical litera- ture. Availability: http://biotea.idiginfo.org, http://biotea.idiginfo.org/gene/

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  • BioJS: An Open Source JavaScript Library For Biological Web 2.0 Applications

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    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 configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by...

    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 configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community.
    Availability: http://code.google.com/p/biojs/

  • Biolinks, semantic characterization of related articles in PubMed Central

    Dasty3, A Web Framework for DAS

    How is a scientific article related to another scientific article? how can we characterize a network of related articles?

  • Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of Data

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    This is the semantic infrastructure for PubMed Central.

Projects

  • covid19 knoweldge graph for literature

    - Present

    We are taking all the covid19 related literature and annotating it with some specific ontologies. we are focusing on supporting the construction of conceptual quesries similar to PICO but witin the context of covid19 literature. we are annotationg all the literature with 7 ontologies, our interface makes it possible to select terms that are used in the annotation and establish relations. we proviede a query preview so that users know beforehand what the resulting data set will look like. here...

    We are taking all the covid19 related literature and annotating it with some specific ontologies. we are focusing on supporting the construction of conceptual quesries similar to PICO but witin the context of covid19 literature. we are annotationg all the literature with 7 ontologies, our interface makes it possible to select terms that are used in the annotation and establish relations. we proviede a query preview so that users know beforehand what the resulting data set will look like. here, look like means that users will know in advance the number of documents that could be retreived if the query is executed, what is the cloud of tags describing the resulting data set and also the cloud of authors. users may then choose to re define the query or execute it. if the execute it then they will be able to look at the standard information plus an enriched clud of tags based on the annotations for each paper that allows them to, by mouse over, go the the text snippet that has that term.

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  • knoweldge graphs and ontologies under one roof

    - Present

    we are bridguing the gap between data-ontologies-knowledge graphs.

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  • ontologies and Knowledge graphs in web protege

    - Present

    how could we bridge the gap between ontologies and LPGs?

    See project

  • biotea

    - Present

    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 Social Web have barely made an impact on scientific communication.

    We present our approach to scholarly communication within the context of the Semantic Web...

    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 Social Web have barely made an impact on scientific communication.

    We present our approach to scholarly communication within the context of the Semantic Web, which entails understanding the research paper as an interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive reuse of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/

    The semantic processing for biomedical literature that we present in this paper embeds documents in the Web of Data and facilitates the execution of concept-based queries over the entire digital library. Moreover, our approach delivers a flexible and adaptable semantic infrastructure for digital libraries; it is applicable independently of the business model of the publisher. Our model delivers a semantically rich and highly linked dataset with self-describing content so that software can make effective use of it.

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Languages

  • Spanish

    -

  • English

    Full professional proficiency

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