q Luana Licata’s fellowship report – ISB (Biocuration)

Luana Licata’s fellowship report

By Luana Licata

The short-term fellowship conferred by the International Society for Biocuration (ISB) has given me the opportunity to spend, as a visitor, two weeks, from the 2nd to the 13th of July 2018, at the EMBL-EBI, Hinxton, UK.

At the EMBL-EBI, I have been hosted by the IntAct team and I have worked with the Protein Function Team (EMBL-EBI) and the Gene Annotation Team of the Centre for Cardiovascular Genetics (UCL, London) and with the Molecular Interaction Team (IntAct, EMBL-EBI).

During my stay, I have been worked on the following topics:

I worked with both Protein Function and Gene Annotation Teams to learn Gene Ontology annotation and how to use Protein2GO. In particular, Ruth Lovering and Rachael Huntley (Gene Annotation, UCL, London) introduced me to GO annotation practices, Extensions and rules and how to use the curation tool, Protein2GO. This has allowed me to start to annotate some proteins and protein relationships involved in the Acute Myeloid Leukemia (AML) pathway already annotated in SIGNOR database, one of the database that I curate at the Bioinformatics and Computational Biology Unit, at University of Rome Tor Vergata. Moreover, with the help of Penelope Garmiri (Protein Function, EMBL-EBI), I had the opportunity to learn the basis of NOCTUA annotation and how to use NOCTUA platform. Noctua annotation allows to combine simple GO annotations in order to generate a network of annotations. This acquired knowledge has allowed me to start to annotate, at a basic level, also in NOCTUA platform some relationships relevant to Acute Myeloid Leukemia (AML) pathway coming form SIGNOR database in order to be able to produce some GO-CAM models. GO-CAM models are the models produced with Noctua. The final goal of this collaboration has been not only to improve and enhance knowledge about current GO annotation practice but also to be able, in the next future, to represent and compare information relevant to the AML pathway that I have annotated in different ways, such as SIGNOR, GO and NOCTUA annotation.

I worked with the Molecular Interaction Team to further develop protein-nucleic acid interaction annotation in MINT database. In particular, I have learned how biocurators in the Molecular Interaction Team capture information about protein-nucleic acid interactions and I have annotated in the IntAct editor (IntAct curation tool) articles containing information on the interaction between transcription factor and transcribed gene. Moreover, during my visit, working in close contact with colleagues from the molecular interaction team has allowed to strengthen the work of the MINT database (the other database that I coordinate and curate) inside the IMEx Consortium through a better curation coordination.