A synthesis of omics, pathway, systems biology brings us to the next level of proactive drug discovery. SemWeb architecture enables uncoordinated collaboration and connects to growing fabric of highly connected data and text.
Biologists, chemists and health care informaticians have modeled vast swaths of biological function, chemical compound and disease data into public Linked Data repositories. Complementing this with proprietary stores of biomarker, pathway and more evolved biological models knits these sources together to more effectively answer investigation and discovery queries.
Structured Experimental Results
The panacea of complete, recall-able coding of all institutional knowledge is, of course, out of reach. A representation which encourages/enables unambiguous recall, combined with a strategic assessment of assets, provides a linear value proposition for evolving towards a more re-usable information infrastructure. For example, one can initially simply record that an experiment demonstrated an upregulation of a protein in the presence of a compound, and, as needs or sequencing output evolve, qualify that upregulation with factors and necessary conditions. This coded knowledge can travel from lab notebooks to publications to institutional archive.
Increasingly, experimental protocols and findings are traded or shared in limited partnerships or acquired. Such partnerships require interpretation by parties without time for culture share between collaborating parties. A course capture of experimental meta data and results can show immediate value and motivate incremental precision as use cases motivate.
In addition to experimental results, researchers need to efficiently search for and access literature and patents. The SWAN and SIOC ontologies associate theories and evidence with publications, and ORB exposes the structure of the document with assertions potentially embedded in the document itself.
There is a move to have FDA release "comparator arm" data from clinical trials. This is data that is gathered as part of a new drug investigation, but isn't related to the new drug - it's comparison data about either on-market drugs or the state of the disease. Either way it is not competitive to the pharma that collected it. Once this data starts to move out onto the web there will be a huge pull to integrate with it. Getting the standards right for formatting, querying, and dealing with it will be huge, and the companies that are at the table will be the best equipped to use the data first.
Patient Data Ownership
Patients are increasingly capturing their own data, from classic health record information (V.A. "blue button") to modern versions of health info (Patients Like Me, Cure Together) to genomic information (23andme). There are no good standards to federate data from across this chain into a cohesive, usable and integrated system. If pharma doesn't create this as a standard, the odds are good that it will be a private standard à la Facebook and they extract high rents from those who need access to large populations for clinical molecular profiling (i.e., pharma). Biotech Acquisition
Web standards, especially RDF/OWL/SPARQL, can ease the process of due diligence in a complex scientific data business. Pharmas constantly acquire projects, products, biotech companies, and each other. They are constantly forming alliances via contract with each other, and the vast majority of the underlying information would be far easier to integrate if stored in web formats. This is work that is much less exploratory than the current HCLS work, as these data formats are already well worked out and the economic imperative to lower the time it takes either to make an acquisition or to complete it is high.
Supply Chain Automation
As the complexity of process input and product interaction grows, business modelers will need more autonomy in describing their domains. While this is true in many domains, it's particularly salient to workflows which consume and produce unstable goods such as biologics. Exploitation of RDF's distributed extensibility model will enable less centralized, more functional modeling of business processes, output from new instruments, and evolving understanding of chemical/biological processes. This effectively moves the information from the Electronic Lab Notebook into the operations domain, using scientific knowledge to identify costs and bottlenecks and drive improved accounting.
Risk distribution and inefficiencies introduced by redundant development efforts are driving the pharmaceutical industry towards cooperative development infrastructure like Arch2POCM. The ideas of such a FIPNet (Fully Integrated Pharmaceutical Network) are best realized with a shared, extensible model data and resources. Invested parties will focus on their core competencies, exposing the research assets they develop with other parties for further development or oversight.
@@merge with Collaborative R&D?
pharmas increasingly partnering with other pharmas and/or biotechs to develop new therapies.
- new compounds - identification of new targets in a disease area - collabporation in a therapeutic area (e.g. Pfizer and GSK)
Clinical, municipal and nongovernmental agencies negotiate their own reporting contracts with monitoring agents. Likewise, regulatory bodies must respond flexibly to different reporting formats and information spaces. The Semantic Web offers consistent access to data regardless of whether the structure of that data has been standardized by a sanctioned organization or it has not yet gone through the standards process. This allows organizations to focus their standardization efforts on components key to early use cases and let other standards be developed or discovered by concerned parties.
Easing the mismatches between data models and encoding systems will enable much more rigorous review of health outcomes by health care providers, drug/therapy developers, and monitoring agencies. Clinicians and pharmaceuticals can cooperate to provide more informed therapy prescriptions, and pharmaceuticals can learn of markets for new compounds and off-label prescriptions.
@@Web Integration (delete me?)
The grounding of the Semantic Web promotes the integration of the assertional framework with conventional web architecture and tools. The ubiquity of tools supporting Web standards like HTML and XPath enables one to associate structured knowledge with regions of documents, communicating simultaneously in languages tailored to humans and machines. Web architecture has permeated our society; scientists and technicians need little or no training to use systems which are based on the familiar web browsing experience. The extension of this architecture to support not just resource linking and annotations but a fabric of structured knowledge will be the easiest transition into deep knowledge capture.
Clinical Decision Support