Annotating Molecular Interactions in MINT

1. Annotating Molecular Interactions in MINT http://mint.bio.uniroma2.it/mint/Welcome.do

2. ANNOTATING PROTEIN INTERACTIONS: STANDARDS AND BASIC ASPECTS

3. What is archived in MINT? • MINT collects P-P interactions experimentally verified • The interaction representation is according to PSI-MIs ontology and nomenclature • The interaction types collected in MINT are: • Colocalizations • Physical interactions • Direct interactions (enzymatic reactions)

4. Curation standards The PSI Molecular Interaction work group develops a common data standard that allows user to retrieve all relevant data from different sites and perform comparative analysis of different datasets

6. Interaction type

7. What is critical in the annotation process? • Organism identification • Proper Uniprot_ID detection • Experimental features annotations • Participant features annotations

8. http://www.nature.com/nbt/consult/index.html

9. Papers selection • Title • Abstract • Materials and methods • Quick look at the figures

11. THE SECOND BIOCREATIVE CHALLENGE: DATASETS PREPARATION

12. MINT curation projects • Journals curation (FEBS letters, EMBO Journal, EMBO Reports) • Thematic curation (Domains, VirHostome)

13. DELIVERED DATASETS • TRAINING SET • (128 pmids 1182 interactions) • TEST SET • (221 pmids 1489 interactions)

14. Biocreative training-set • The MINT/BioCreative positive test set is composed of papers extracted from volumes of FEBS letters, EMBO Journal and EMBO Reports published from january to july 2006 • All the papers not curated from the above mentioned volumes are considered belonging to the negative test set • For each interaction is reported the best interaction description sentence coming out from both the body text and the figure legends

15. ANNOTATION AND PREDICTION: USE CASES

16. Biocreative annotation flaws: examples • FALSE POSITIVES • Phosphorylation • FALSE NEGATIVES • Positive controls • MISINFORMATION • Complexes

17. Use cases • Pol I is a complex • No sentences are available for the illustrated colocalizations In situ colocalization of NM1 and Pol I Immunostaining of isolated nucleoli showed that actin and NM1 were enriched in nucleoli and their distribution correlated with upstream binding factor (UBF) and fibrillarin (Fig 1A). NMI colocalized with Pol I and green fluorescent protein–RPA53, a protein that decorates the active subpopulation of Pol I (Fig 1B). The colocalization between Pol I and NM1 was further corroborated by immunogold electron microscopy using intact HeLa cells (supplementary Fig 1 online). NM1 was distributed throughout the nucleoplasm but was largely excluded from the nucleoli, except the fibrillar centres. These nucleolar subcompartments are known to contain Pol I and Pol I-specific transcription factors (Scheer & Benavente, 1990; Dundr et al, 2002). In addition, both a novel autoimmune serum against Pol I (S57299; see supplementary Figs 2,3 online) and a peptide-specific affinitypurified antibody against NM1 blocked Pol I transcription in vitro (Fig 1C,D). These data support previous studies demonstrating a key role for NM1 in Pol I transcription (Fomproix & Percipalle, 2004; Philimonenko et al, 2004).

18. Use cases This experiment describes a genetic interaction

19. Use cases Post-translational modification or PPI?