2012 08 28 Teleconference Minutes

Databases and Ontologies CoR Teleconference

Draft Minutes

August 28^th, 2012

 

 

 

Participants:

Nathan Baker (Pacific Northwest National Lab), Teresa Fernandes (Heriot-Watt University), Wouter Fransman (TNO), Marty Fritts (SAIC-Frederick, Inc. / NCI at Frederick), Vijay Gupta (RTI International), Fred Klaessig (Pennsylvania Bio Nano Systems, LLC) Rafi Korenstein (Tel Aviv University), Iseult Lynch (University College Dublin), Damaris Murry (RTI International), Krishna Rajan (Iowa State University), Hubert Rauscher (JRC), Stacey Standridge (NNCO)

 

Attachments:

Nanotechnology informatics resources survey results (emailed by Nathan on Aug 25^th)

 

Minutes:

1.  I.            Acknowledgements

The EU FP7 project QNano is supporting this CoR, including hosting the teleconferences and recording the minutes (Iseult Lynch, UCD/QNano). Hubert thanked Iseult on behalf of the CoR, and thanked Stacey for preparing the last set of minutes (Jul 20^th).

1. II.            Scope statement

The text of the proposed scope statement (following the TC on 20^th July 2012) was discussed. The only change suggested was to include modeling in the datasets that would be improved as a result of the CoR (last line of the text).  The final text, as approved by the members of the CoR during the teleconference, is given below:

Interconnected, freely communicating and agreed information systems are urgently needed for collating (a) nanoscale material descriptions; (b) their intrinsic and context-dependent properties and their effects, including environmental and health-related; and (c) their interactions with biological entities. The goal of the US-EU Nanotechnology Databases and Ontology Community of Research (CoR) is to enable the sharing, searching, and analysis of nanoscale material characterization data across a wide range of active and archived experimental sources and to give advice on how to structure these data to enable their widest possible use. Achievement of this goal will deliver important new capabilities to (1) allow integration of pertinent risk assessment data among labs to (2) provide situational awareness of data coverage across nanomaterial categories, and to (3) enable predictive computational models for bridging physical properties and biological outcomes with exposure, dispersal and fate.  In order to realize this goal, the Community of Research will initially focus on the following three areas of investigation:

• Identification of the data elements necessary to establish common data-sharing model(s) for this domain.
• Specification of requirements for sharing data between research groups and repositories in human- and machine-interpretable forms
• Definition of concepts necessary to support the above activities and representation of those concepts in an ontological framework. This will include characterizers for the material itself as well as descriptors for its interaction with the environment and elements to characterize intermediate effects in adverse outcome pathways.

Through these activities the CoR will provide tools for improving the overall quality of experimental and modeling data being generated in the research communities in the EU and US.

1. III.            Resource Inventory

The results of the internet survey were summarized by Nathan:  it is currently very much a work in progress, and, as he added several himself it is currently US-biased, so we need to address this by identifying and adding additional resources to the inventory, verbally, via email or via the webform.

As a reminder of why we are gathering this information: As per scope statement (see above) we have three areas of investigation (Identification of data elements for sharing, Specification of requirements, and Definition of concepts) – all 3 elements require situational awareness of existing resources to identify end-points for sharing.  Thus, we want to ensure that the inventory is as complete as possible.

Summary of entries:

caNanoLab– database at NCI – focused on nanomedicine, but also EHS data – cellular and NP-physico-chemial data.

NanoParticle Ontology (NPO) – US-NHI funded, maintained by NMI WG led by Nathan Baker. Open to use and expand. Based on formal upper level ontology and best practice.

Institute of Future Technologies (IFT) – Database, Ontology, taxonomy, or other vocabulary, Search engine, Analysis software, data integration, processing and analysis. (Axel Mustard in hospital)

JRC NANOhub – based on IUCLID (used in EU for registration of chemicals), with additional nano-specific endpoints added.  Can be used (on voluntary basis) by any project researching safety.  Individual installations are not public.  OECD WPMN use in sponsorship programme on NMs.

DaNa Knowledge Base– taxonomy / ontology.  Materials centric. Interesting layout – search by commercial application, materials in those applications, then exposure, uptake and risk factors.  Industry contributions also, consumer-driven. Not sure if accessible /open.

Nanomaterial Registry – Clearinghouse – canonical information about NMs from multiple sources.  Also a scoring of the data, including use of appropriate controls etc.  Minimal information required to characterize NMs.  The curation involves application of designed terminology to pick out the information that is required.  Also used to interpret terms used into the control vocabulary.

InterNano – hosts unstructured data describing nanomaufacturing and nanotechnologies – industrial focus, well developed taxonomy for annotation, browsing and navigation.

ICON –home to several different resources.  Primarily database-like focused on EHS. International industry coalition sponsored.

Nanomaterial-Biological Interactions Knowledgebase – US agencies – environmental EHS – structured endpoints, exposure of NMs in model organisms / systems. 

Bioportal – not nano-specific, but an important resource to include.  Crowd-sourced approach to ontology – 100-150 ontologies that can be searched, and used.  Nanotech term scattered in sub-sets of these ontologies (10-20 ontologies).

GoodNanoGuide – unstructured resource – review and informational material, educational EHS material, focus on workplace and workers.

ISA-TAB nano – format for sharing data between resources, based on ISA-TAB standard.  EBI-Oxford group.

List of other resources…at the bottom. Note also TNO submitted the following:

NECID (Nano Exposure and Contextual Information Database) – Occupational exposure database – collate and share Occupational exposure data among institutes in Europe.

The subsequent discussion resulted in identification of several other resources that can be added (see below) and in agreement to establish a data-sharing system that all CoR members can use to make the Resources document a living document.  QNano utilize a portal called TeamLab (a free open-source platform for collaboration and project management) and will make a TeamLab site for the Databases and Ontologies CoR available for this and other CoR activities.  This can later be linked to the official website (currently www. US-EU.org).

Missing resources heard about in Grenoble (May 2012), and at the NanoSafetyCluster WG4 (Databases) meeting in Dublin in March 2012, such as:

–       NHECD (critical, commented database of literature) – Rafi’s commented database, which will be hosted by the JRC.  This will be ready in ~1 month, will be added then.

–       dbAlm: Database on alternative tests – ECVAM

–       NERC’s Handlebar

–       Could also add something on the Nanosafety cluster WG on databases which represents all the EU FP7 projects with a database component.

Action items: 

• Follow-up with potential contributors
• Iseult to set up TeamLab for the CoR.

 

1. IV.            Helsinki workshop half day session discussion

The second EU-U.S.: Bridging NanoEHS Research Efforts workshop will be held in Helsinki, Finland on October 25-26, 2012 and is being organized by DG RTD. The primary focus of the workshop will be building up the six Communities, with a breakout session on each CoR theme. Each CoR is responsible for nominating 1 rapporteur and 2 speakers for their breakout session.

The Databases & Ontology CoR will have a ½ day session, including an Introduction to the scope of the CoR and 1 presentation from US side / 1 presentation from EU side.  These should be overview presentations on the relevant activities in the two geographical areas. 

EU part – Hubert suggested an overview presentation of the nano database / ontology situation in EU as represented by the NanoSafety Cluster WG on databases (Chairs:  Iseult Lynch / Teresa Fernandes).  This was agreed by all.  

US side: Not discussed.

 

1. V.                   Special journal issue in Computation Science & Discovery

The US-EU CoR is a great opportunity to develop papers to focus on EU-US collaboration, and independent activities in the areas of databases, ontologies, modeling activities as related to nanoEHS.  Review articles and/or original research contributions welcome.

This is an open invitation to contribute for Database & Ontologies CoR members.  If interested, please contact Hubert & Nathan with a suggested title for your contribution so they get an idea of how large / small the issue might be.

Timing:  kick-off in fall after the Helsinki meeting.

Broaden to include other relevant CoRs: Ecotoxicity Testing and Predictive Models (EU chair: Henriette Selck, US chair:  Steve Klaine) and Predictive Modeling for Human Health (EU chair: Bengt Fadeel, US chair: Yoram Cohen).

Should also include a good critique / critical review of what is needed / missing to enable experimentalists & modelers to engage more closely: e.g., modellers describing why they don’t have enough experimental data / experimentalists saying why they can’t apply / understand models => what is missing and how the gaps can be bridged. Also include critical assessment of how to link up the various aspects – build on the expertise in the existing group and see that we actually do make some suggestions on how to move beyond the existing status.

Action items:

• Nathan & Hubert to draft a short paragraph describing the special issue and send to Chairs of the other CORs and the members of this group – include language that encourages cross-talk. 

 

VI.         Any Other Business

Proposed an action item on assessing ruggedness of testing data – (sensitivity of model / protocol to variability).  Very little literature on consistent data sets, or about how sensitive methods are – i.e. if you change a reagent does that affect the assay outcome?

Vijay recalls one paper: even small differences in protocol resulted in very different data.

QNano is looking at assay sensitivity in terms of which assay for a given end-point is most sensitive for nanomaterials, and within a given assay how much a nanomaterial’s physico-chemical properties can be varied before the assay gives a significantly different outcome, and how much can you vary the NM in terms of a specific parameter for it to still be recognized by cellular assays as same NM.

IRMM effort – certification of a NM: Outcome of inter-laboratory comparison  is part of the certification exercise. Related to robustness of methods.

Action items:

• Everyone to send papers on this to Nathan / Hubert who will distribute.
• This topic will then be discussed further in subsequent meetings.