Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. - Alexander García Castro; Samuel Thoraval; Leyla J. García; Mark A. Ragan (BMC Bioinform., 2005)

CMAPS Supporting the Development of OWL Ontologies. - Alexander García Castro; Angela Norena; Andres Betancourt; Leyla J. García (ISWC (Posters & Demos), 2008)

Annotating Atomic Components of Papers in Digital Libraries: The Semantic and Social Web Heading towards a Living Document Supporting eSciences. - Alexander García Castro; Leyla Jael García Castro; Alberto Labarga; Olga L. Giraldo; César Montaña; Kieran O'Neill; John A. Bateman (DEXA, 2009)

Tags4Tags: Using Tagging to Consolidate Tags. - Leyla Jael García Castro; Martin Hepp; Alexander García Castro (DEXA, 2009)

TagSorting: A Tagging Environment for Collaboratively Building Ontologies. - Leyla Jael García Castro; Martin Hepp; Alexander García Castro (EKAW, 2010)

Using the Annotation Ontology in Semantic Digital Libraries. - Leyla Jael García Castro; Olga L. Giraldo; Alexander García Castro (ISWC (Posters & Demos), 2010)

Semantic Web and Social Web heading towards Living Documents in the Life Sciences. - Alexander García Castro; Alberto Labarga; Leyla J. García; Olga L. Giraldo; César Montaña; John A. Bateman (J. Web Semant., 2010)

Developing Ontologies within Decentralised Settings. - Alexander García Castro; Kieran O'Neill; Leyla Jael García Castro; Phillip W. Lord; Robert Stevens 001; Óscar Corcho; Frank Gibson (Semantic e-Science, 2010)

Annotating Experimental Records Using Ontologies. - Alexander García Castro; Olga L. Giraldo; Leyla J. García (ICBO, 2011)

Tagsty: augmented knowledge from community-based annotations on protein sequences. - Leyla Jael García Castro; Alexander García Castro (SWAT4LS, 2011)

A translational model for representing research articles. - Alexander García Castro; Leyla Jael García Castro (SWAT4LS, 2011)

Dasty3, a WEB framework for DAS. - Jose M. Villaveces; Rafael C. Jiménez; Leyla J. García; Gustavo A. Salazar; Bernat Gel; Nicola J. Mulder; Maria Jesus Martin; Alexander García Castro; Henning Hermjakob (Bioinform., 2011)

An open annotation ontology for science on web 3.0. - Paolo Ciccarese; Marco Ocana; Leyla Jael García Castro; Sudeshna Das 001; Tim Clark (J. Biomed. Semant., 2011)

Using annotations to model discourse: an extension to the Annotation Ontology. - Leyla Jael García Castro; Olga L. Giraldo; Alexander García Castro (SePublica@ESWC, 2012)

Conceptual Exploration of Documents and Digital Libraries in the Biomedical Domain. - Leyla Jael García Castro; Alexander García Castro; John Gómez (SWAT4LS, 2012)

Connections across Scientific Publications based on Semantic Annotations. - Leyla Jael García Castro; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann; Alexander García Castro (SePublica, 2013)

BioJS: an open source JavaScript framework for biological data visualization. - John Gómez; Leyla J. García; Gustavo A. Salazar; Jose M. Villaveces; Swanand P. Gore; Alexander García Castro; Maria Jesus Martin; Guillaume Launay; Rafael Alcántara; Noemi del-Toro; Marine Dumousseau; Sandra E. Orchard; et al. (Bioinform., 2013)

Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. - Leyla Jael García Castro; Casey McLaughlin; Alexander García Castro (J. Biomed. Semant., 2013)

Social Tags and Linked Data for Ontology Development: A Case Study in the Financial Domain. - Andrés García-Silva; Leyla Jael García Castro; Alexander García Castro; Óscar Corcho (WIMS, 2014)

The EBI RDF platform: linked open data for the life sciences. - Simon Jupp; James Malone; Jerven T. Bolleman; Marco Brandizi; Mark Davies; Leyla J. García; Anna Gaulton; Sebastien Gehant; Camille Laibe; Nicole Redaschi; Sarala M. Wimalaratne; Maria Jesus Martin; et al. (Bioinform., 2014)

BioJS: an open source standard for biological visualisation - its status in 2014. - Manuel Corpas; Rafael C. Jiménez; Seth Carbon; Alexander García Castro; Leyla Jael Castro; Tatyana Goldberg; John Gómez; Alex Kalderimis; Suzanna E. Lewis; Ian Mulvany; Aleksandra Pawlik; Francis Rowland; et al. (F1000Research, 2014)

Building Domain Ontologies Out of Folksonomies and Linked Data. - Andrés García-Silva; Leyla Jael García Castro; Alexander García Castro; Óscar Corcho (Int. J. Artif. Intell. Tools, 2015)

In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access. - Leyla Jael García Castro; Rafael Berlanga Llavori; Alexander García Castro (J. Biomed. Informatics, 2015)

A Graph-based Taxonomy RESTful Data Service. - Leyla J. García; Leonardo Gonzales; Maria Jesus Martin (SWAT4LS, 2016)

Bioschemas: schema.org for the Life Sciences. - Leyla J. García; Olga L. Giraldo; Alexander García Castro; Michel Dumontier; Bioschemas Community (SWAT4LS, 2017)

ProtVista: visualization of protein sequence annotations. - Xavier Watkins; Leyla J. García; Sangya Pundir; Maria Jesus Martin; UniProt Consortium (Bioinform., 2017)

Four simple recommendations to encourage best practices in research software. - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

Biotea-Biolinks: A semantic infrastructure for exploring and analyzing scientific publications. - Leyla Jael Castro (2017)

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars. - Denise Carvalho-Silva; Leyla J. García; Sarah L. Morgan; Cath Brooksbank; Ian Dunham (PLoS Comput. Biol., 2018)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Overview of LiLAS 2020 - Living Labs for Academic Search. - Philipp Schaer; Johann Schaible; Leyla Jael García Castro (CLEF, 2020)

Overview of LiLAS 2020 - Living Labs for Academic Search Workshop Lab (extended abstract). - Philipp Schaer; Johann Schaible; Leyla Jael García Castro (CLEF (Working Notes), 2020)

Towards semantic representation of machine-actionable Data Management Plans. - João Cardoso 002; Leyla J. García; Fajar J. Ekaputra; Marie C. Jacquemot; Tomasz Miksa; José Borbinha (DaMaLOS, 2020)

Software as a first-class citizen in research. - Leyla J. García; Michelle Barker; Neil P. Chue Hong; Fotis E. Psomopoulos; Jennifer L. Harrow; Daniel S. Katz; Mateusz Kuzak; Paula Andrea Martínez; Allegra Via (DaMaLOS, 2020)

GlyGen data model and processing workflow. - Robel Y. Kahsay; Jeet Vora; Rahi Navelkar; Reza Mousavi; Brian C. Fochtman; Xavier Holmes; Nagarajan Pattabiraman; René Ranzinger; Rupali Mahadik; Tatiana Williamson; Sujeet Kulkarni; Gaurav Agarwal; et al. (Bioinform., 2020)

Towards FAIR principles for research software. - Anna-Lena Lamprecht; Leyla J. García; Mateusz Kuzak; Carlos Martinez-Ortiz; Ricardo Arcila; Eva Martin Del Pico; Victoria Dominguez Del Angel; Stephanie van de Sandt; Jon C. Ison; Paula Andrea Martínez; Peter McQuilton; Alfonso Valencia; et al. (Data Sci., 2020)

39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition. - Caterina Caracciolo; Sophie Aubin; Clément Jonquet; Emna Amdouni; Romain David 001; Leyla J. García; Brandon Whitehead; Catherine Roussey; Armando Stellato; Ferdinando Villa (Data Sci. J., 2020)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)

Ten simple rules to run a successful BioHackathon. - Leyla J. García; Erick Antezana; Alexander García Castro; Evan Bolton; Rafael C. Jiménez; Pjotr Prins; Juan M. Banda; Toshiaki Katayama (PLoS Comput. Biol., 2020)

Ten simple rules for making training materials FAIR. - Leyla J. García; Bérénice Batut; Melissa L. Burke; Mateusz Kuzak; Fotis E. Psomopoulos; Ricardo Arcila; Teresa K. Attwood; Niall Beard; Denise Carvalho-Silva; Alexandros C. Dimopoulos; Victoria Dominguez Del Angel; Michel Dumontier; et al. (PLoS Comput. Biol., 2020)

Overview of LiLAS 2021 - Living Labs for Academic Search (Extended Overview). - Philipp Schaer; Timo Breuer 002; Leyla Jael Castro; Benjamin Wolff; Johann Schaible; Narges Tavakolpoursaleh (CLEF (Working Notes), 2021)

Overview of LiLAS 2021 - Living Labs for Academic Search. - Philipp Schaer; Timo Breuer 002; Leyla Jael Castro; Benjamin Wolff; Johann Schaible; Narges Tavakolpoursaleh (CLEF, 2021)

Working Towards Understanding the Role of FAIR for Machine Learning. - Daniel S. Katz; Fotis E. Psomopoulos; Leyla Jael Castro (DaMaLOS, 2021)

Living Lab Evaluation for Life and Social Sciences Search Platforms - LiLAS at CLEF 2021. - Philipp Schaer; Johann Schaible; Leyla Jael Castro (ECIR (2), 2021)

Ontology Clustering with OWL2Vec. - Ashley Ritchie; Jiaoyan Chen 001; Leyla Jael Castro; Dietrich Rebholz-Schuhmann; Ernesto Jiménez-Ruiz (DeepOntoNLP/X-SENTIMENT@ESWC, 2021)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

Embeddings of Gene Ontology (GO) using OWL2Vec. - Ashley Ritchie; Jiaoyan Chen 001; Leyla Jael Castro; Dietrich Rebholz-Schuhmann; Ernesto Jiménez-Ruiz (Zenodo, 2021)

Results of the Ontology Alignment Evaluation Initiative 2022. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; Yuan He 008; Ian Horrocks 001; et al. (OM@ISWC, 2022)

DCSO: towards an ontology for machine-actionable data management plans. - João Cardoso 002; Leyla Jael Castro; Fajar J. Ekaputra; Marie C. Jacquemot; Marek Suchánek; Tomasz Miksa; José Borbinha (J. Biomed. Semant., 2022)

Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. - Bernd Müller; Leyla Jael Castro; Dietrich Rebholz-Schuhmann (J. Biomed. Semant., 2022)

Online Information Retrieval Evaluation using the STELLA Framework. - Timo Breuer 002; Narges Tavakolpoursaleh; Johann Schaible; Daniel Hienert; Philipp Schaer; Leyla Jael Castro (CoRR, 2022)

Packaging research artefacts with RO-Crate. - Stian Soiland-Reyes; Peter Sefton; Mercè Crosas; Leyla Jael Castro; Frederik Coppens; José María Fernández 001; Daniel Garijo; Björn A. Grüning; Marco La Rosa; Simone Leo; Eoghan Ó Carragáin; Marc Portier; et al. (Data Sci., 2022)

Enhancing Reproducibility in Research Through FAIR Digital Objects. - Zeyd Boukhers; Leyla Jael Castro (CoRDI, 2023)

Schema.org as a Lightweight Harmonization Approach for NFDI. - Leyla Jael Castro; Juliane Fluck; Daniel Arend; Matthias Lange 001; Daniel Martini; Steffen Neumann; Sonja Schimmler; Dietrich Rebholz-Schuhmann (CoRDI, 2023)

RO-Crates Meets FAIR Digital Objects. - Leyla Jael Castro; Stian Soiland-Reyes; Dietrich Rebholz-Schuhmann (CoRDI, 2023)

Machine-Actionable Metadata for Software and Software Management Plans for NFDI. - Olga L. Giraldo; Danilo Dessì; Stefan Dietze; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (CoRDI, 2023)

Harmonising, Harvesting, and Searching Metadata Across a Repository Federation. - Steffen Neumann; Felix Bach; Leyla Jael Castro; Tillmann Fischer; Stefan Hofmann; Pei-Chi Huang; Nicole Jung; Bhavin Katabathuni; Fabian Mauz; René Meier 002; Venkata Chandrasekhar Nainala; Noura Rayya; et al. (CoRDI, 2023)

DaMaLOS 2023 Editorial Note. - Leyla Jael Castro; Dietrich Rebholz-Schuhmann; Danilo Dessì; Jens Dierkes; Sonja Schimmler (DaMaLOS, 2023)

A metadata schema for machine-actionable Software Management Plans. - Leyla Jael Castro; Dietrich Rebholz-Schuhmann; Nelson Quiñones; Dimitrios Bampalikis; Olga L. Giraldo; Eva Martin Del Pico; Allegra Via; Dhwani Solanki; Lukas Geist; Fotis E. Psomopoulos; Renato Alves; José María Fernández González (DaMaLOS, 2023)

A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus. - Rohitha Ravinder; Tim Fellerhoff; Vishnu Dadi; Lukas Geist; Guillermo Rocamora; Muhammad Talha 004; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (SeWeBMeDA@ESWC, 2023)

Research Knowledge Graphs in NFDI4DS. - Saurav Karmakar; Matthäus Zloch; Fidan Limani; Benjamin Zapilko; Sharmila Upadhyaya; Jennifer D'Souza 001; Leyla Jael Castro; Georg Rehm; Marcel R. Ackermann; Harald Sack; Zeyd Boukhers; Sonja Schimmler; et al. (GI-Jahrestagung, 2023)

NFDI4DS Infrastructure and Services. - Sonja Schimmler; Bianca Wentzel; Arnim Bleier; Stefan Dietze; Saurav Karmakar; Peter Mutschke; Angelie Kraft; Tilahun Abedissa Taffa; Ricardo Usbeck; Zeyd Boukhers; Sören Auer; Leyla Jael Castro; et al. (GI-Jahrestagung, 2023)

Results of the Ontology Alignment Evaluation Initiative 2023. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Adrien Coulet; Julien Cufi; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; et al. (OM@ISWC, 2023)

A metadata analysis for machine-actionable Software Management Plans. - Olga L. Giraldo; Renato Alves; Dimitrios Bampalikis; José M. Fernández; Eva Martin Del Pico; Fotis E. Psomopoulos; Nelson Quiñones; Dhwani Solanki; Allegra Via; Leyla Jael Castro (SWAT4HCLS, 2023)

Document-to-document relevance assessment for TREC Genomics Track 2005. - Olga L. Giraldo; María Fernanda Cadena; Andrea Robayo-Gama; Dhwani Solanki; Tim Fellerhoff; Lukas Geist; Rohitha Ravinder; Muhammad Talha 004; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (SWAT4HCLS, 2023)

Multilabel-classification task for Medline abstracts. - Nelson Quiñones; Cesar Canales; Javier Torres; Dietrich Rebholz-Schuhmann; Leyla Jael Castro; Andrés Aristizábal (SWAT4HCLS, 2023)

Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks. - Rohitha Ravinder; Leyla Jael Castro; Martin Hofmann-Apitius; Dietrich Rebholz-Schuhmann (SWAT4HCLS, 2023)

OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus. - Rohitha Ravinder; Tim Fellerhoff; Vishnu Dadi; Lukas Geist; Guillermo Rocamora; Muhammad Talha 004; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (SWAT4HCLS, 2023)

Foundational Competencies and Responsibilities of a Research Software Engineer. - Florian Goth; Renato Alves; Matthias Braun 005; Leyla Jael Castro; Gerasimos Chourdakis; Simon Christ; Jeremy Cohen 002; Fredo Erxleben; Jean-Noël Grad; Magnus Hagdorn; Toby Hodges; Guido Juckeland; et al. (CoRR, 2023)

An Analysis of Crosswalks from Research Data Schemas to Schema.org. - Mingfang Wu; Stephen M. Richard; Chantelle Verhey; Leyla Jael Castro; Baptiste Cecconi; Nick S. Juty (Data Intell., 2023)

Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources. - Leyla Jael Castro; Patricia M. Palagi; Niall Beard; Teresa K. Attwood; Michelle D. Brazas (PLoS Comput. Biol., 2023)

Correction: 39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition. - Caterina Caracciolo; Sophie Aubin; Clément Jonquet; Emna Amdouni; Romain David 001; Leyla J. García; Brandon Whitehead; Catherine Roussey; Armando Stellato; Ferdinando Villa (Data Sci. J., 2023)

Towards metadata for machine learning - Crosswalk tables. - Leyla Jael Castro; Fynn Beuttenmüller; Zongxiong Chen; Sefika Efeoglu; Daniel Garijo; Fotis E. Psomopoulos; Beatriz Serrano-Solano; Kirubel Biruk Shiferaw; Dhwani Solanki; Bianca Wentzel; Yue Zhang 069 (Zenodo, 2023)

A Lightweight Approach to FDOs via Bioschemas, RO-Crate and Signposting on GitHub Pages. - Rohitha Ravinder; Nelson Quiñones; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (FDO, 2024)

Practical webby FDOs With RO-Crate and FAIR Signposting Experiences and Lessons Learned. - Stian Soiland-Reyes; Peter Sefton; Simone Leo; Leyla Jael Castro; Claus Weiland; Herbert Van de Sompel (FDO, 2024)

Designing a FAIRification game for Research Software. - Rohitha Ravinder; Dhwani Solanki; Claudio Carta; Bruna dos Santos Vieira; Johannes Keller 006; Marco Roos; Leyla Jael Castro (SWAT4HCLS, 2024)

MLentory, an FDO registry for machine learning models. - Dhwani Solanki; Nelson Quiñones; Dietrich Rebholz-Schuhmann; Leyla Jael Castro (SWAT4HCLS, 2024)

Synthetic data: How could it be used for infectious disease research? - Styliani-Christina Fragkouli; Dhwani Solanki; Leyla Jael Castro; Fotis E. Psomopoulos; Núria Queralt-Rosinach; Davide Cirillo; Lisa C. Crossman (CoRR, 2024)

Research Knowledge Graphs: The Shifting Paradigm of Scholarly Information Representation. - Matthäus Zloch; Danilo Dessì; Jennifer D'Souza 001; Leyla Jael Castro; Benjamin Zapilko; Saurav Karmakar; Brigitte Mathiak; Markus Stocker; Wolfgang Otto 002; Sören Auer; Stefan Dietze (ESWC (2), 2025)

Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences. - Gavin Farrell; Eleni Adamidi; Rafael Andrade Buono; Mihail Anton; Omar Abdelghani Attafi; Salvador Capella-Gutiérrez; Emidio Capriotti; Leyla Jael Castro; Davide Cirillo; Lisa C. Crossman; Christophe Dessimoz; Alexandros C. Dimopoulos; et al. (CoRR, 2025)