Annotating Molecular Interactions in MINT

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Annotating Molecular Interactions in MINT
http//mint.bio.uniroma2.it/mint/Welcome.do
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ANNOTATING PROTEIN INTERACTIONS STANDARDS AND
BASIC ASPECTS
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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)

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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
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Interaction type
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What is critical in the annotation process?

• Organism identification
• Proper Uniprot_ID detection
• Experimental features annotations
• Participant features annotations

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http//www.nature.com/nbt/consult/index.html
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Papers selection

• Title
• Abstract
• Materials and methods
• Quick look at the figures

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THE SECOND BIOCREATIVE CHALLENGE DATASETS
PREPARATION
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MINT curation projects

• Journals curation (FEBS letters, EMBO Journal,
  EMBO Reports)
• Thematic curation (Domains, VirHostome)

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

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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

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ANNOTATION AND PREDICTION USE CASES
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Biocreative annotation flaws examples

• FALSE POSITIVES
• Phosphorylation
• FALSE NEGATIVES
• Positive controls
• MISINFORMATION
• Complexes

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Use cases

1. Pol I is a complex
2. 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
proteinRPA53, 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 an
tibody 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).
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Use cases
This experiment describes a genetic interaction
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Use cases
Post-translational modification or PPI?