MINT, the molecular interaction database: 2009 update

MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium

Deterioration of stone and mineral materials from the Roman Imperial “Cilla of the Antonines” at ancient lanuvium

The “Villa of the Antonines”, located at the 18th mile of the ancient Via Appia, is so far the least explored of the ancient Roman imperial residences in the area of the Alban Hills. Excavations at “Villa of the Antonines” permit an investigation of subsurface deterioration of cultural stone, addressing two primary questions: (1) What are the deterioration processes in the soil and sediment environment, and how do these compare to subaerial deterioration processes? (2) How might the deterioration impact other methodologies reliant on the analysis of the material, such as use and wear analysis, dating techniques, and provenience by chemical tracers? The deterioration characteristics of materials recovered thus far can be visually described. Marbles are discolored and exhibit a loss of polish and partial to extensive granular disintegration and powdering. Brick varies in color and composition due to manufacturing and material differences, but may also exhibit within-soil alteration. Glass tesserae exhibit frosting and pitting from chemical solution. Scanning electron microscopy (SEM) reveals surface microdeterioration such as pitting, etching, and glazing. Qualitative backscatter electron microscopy (BSEM) and energy dispersive spectroscopy (EDS) indicate the distribution of elements, including byproducts of chemical deterioration, likely within the soil environment

DOMINO: a database of domain–peptide interactions

Many protein interactions are mediated by small protein modules binding to short linear peptides. DOMINO () is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. DOMINO can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions

MINT: the Molecular INTeraction database

The Molecular INTeraction database (MINT, ) aims at storing, in a structured format, information about molecular interactions (MIs) by extracting experimental details from work published in peer-reviewed journals. At present the MINT team focuses the curation work on physical interactions between proteins. Genetic or computationally inferred interactions are not included in the database. Over the past four years MINT has undergone extensive revision. The new version of MINT is based on a completely remodeled database structure, which offers more efficient data exploration and analysis, and is characterized by entries with a richer annotation. Over the past few years the number of curated physical interactions has soared to over 95 000. The whole dataset can be freely accessed online in both interactive and batch modes through web-based interfaces and an FTP server. MINT now includes, as an integrated addition, HomoMINT, a database of interactions between human proteins inferred from experiments with ortholog proteins in model organisms ()

VirusMINT: a viral protein interaction database

Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database (http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein–Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII

The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system’s ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users.National Institutes of Health Office of Research Infrastructure Programs (R01OD010929 to M.T. and K.D.); Canadian Institutes of Health Research (FDN-167277 to M.T.); Canada Research Chair in Systems and Synthetic Biology (to M.T.); National Institutes of Health (2U24HG007822-08, 1R35 GM141873-01 to K.E.R. and C.N.A); Spanish Plan for the Advancement of Language Technology and Proyectos I+D+i2020-AI4PROFHEALTH (PID2020-119266RA-I00 to M.K.); MITRE (W56KGU-18-D-0004 to L.H. and T.K.). The views, opinions and/or findings contained in this report are those of the authors and should not be construed as an official government position, policy or decision.Peer ReviewedPostprint (published version

The SH2 Domain Interaction Landscape

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells