MODIFICATION
Q -- Phenotype mapping algorithm and tools for recording human phenotype in ontology terms (Phenotips) and integration of these tools in the National Institutes of Health (NIH), UDP.
- Notice Date
- 7/2/2013
- Notice Type
- Modification/Amendment
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- HHS-NIH-NHLBI-CSB-(HG)-2013-199-DLM
- Archive Date
- 7/24/2013
- Point of Contact
- Dorothy Maxwell, Phone: 301-435-0352
- E-Mail Address
-
maxwelld@mail.nih.gov
(maxwelld@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- A MODIFICATION IS BEING DONE IS TO REMOVE THE FOLLOWING LANGUAGE: This acquisition is being conducted in accordance with the procedures of Simplified Acquisition Procedures (Simplified Acquisition Threshold of $150,000.00) as set forth in FAR Part 13. THIS IS NOT UNDER THE SAT. i. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. ii. The solicitation number is NHLBI-CSB-(HG)-2013-199-DLM and the solicitation is being posted as a request for proposal (RFP). Offerors shall submit their proposals no later than 7:30 a.m. Eastern Standard Time (EST) on July 9, 2013. iii. A statement that the solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-68, June 26, 2013. iv. The associated North American Industry Classification System (NAICS) code for this is 541712, Research and Development in the Physical, Engineering, and Life Sciences (except biotechnology) and small business size standard is 500. PURPOSE: The Contractor shall provide: (1) web service API returning genes and models based on phenotype similarity, (2) a phenotypic similarity approach with PPI, co-expression, etc. to cover cases where an animal model does not yet exist but pheno-copying pathway partners do, (3) an improved of HPO request pipeline, (4) improvements of tools for curating UDP patient phenotypes, and (5) an integration of these tools with the UDP-LIMS. Integration to UDP Laboratory Information Management System (LIMS 24/7) is essential and key. The phenotyping tool within LIMS 24/7, was tailored specifically for UDP by the manufacturer RuRo Inc. Therefore, the Contractor must be familiar and have the ability to integrate with this system. v. Background : The National Human Genome Research Institute (NHGRI), Undiagnosed Disease Program (UDP) is a trans-National Institute of Health (NIH) initiative that focuses on the most puzzling medical cases referred to the NIH Clinical Center in Bethesda, Md. It was organized by the National Human Genome Research Institute (NHGRI), the NIH Office of Rare Diseases Research (ORDR) and the NIH Clinical Center. Many medical specialties from other NIH research centers and institutes contribute the expertise needed to conduct the program, including endocrinology, immunology, oncology, dermatology, dentistry, cardiology and genetics, among the dozens of participating senior attending physicians. A longstanding medical condition that eludes diagnosis by a referring physician can be considered undiagnosed and may be of interest to this clinical research program. The Undiagnosed Disease Program (UDP) offers patients the hope of a diagnosis and the possibility of therapeutic strategies. In return, patients provide UDP researchers the opportunity to gain new insights about genetic and biochemical mechanisms of disease and insights into normal cell biology, biochemistry and physiology. So far, UDP researchers have encountered patients with uncommon presentations of known disorders, multi-systemic complex disorders and new disorders that have never been diagnosed. UDP clinical researchers are using advances in DNA sequencing to detect defects in genes that point to known disorders. These tools offer the potential for discoveries about the role of molecular and biochemical events that can cause disease and, eventually, the development of diagnostic and therapeutic approaches for rare and common diseases. Objective: • Provide a robust methodology for recording patient phenotypes in the standardized and robust human phenotype ontology nomenclature, provide a real time mapping of those terms to known human diseases and model organisms (fly, mouse, zebrafish, and worm), and provide a tool for prioritizing exome and genome sequence variants according to phenotype. CONTRACTOR REQUIREMENTS : A. Specific Tasks : 1. Similarity algorithm will use human, fly, mouse, zebrafish, and worm phenotypes. The service will be based on OWLSim (http://owlsim.org). The Government will provide a web service layer that will be deployable using any standard servlet container (TomCat, Jetty). 2. Widget-style development suitable for integration into Phenotips (dependent on Phenotips to call the API) 3. Visualization and evidence for the matches 4. Identify researchers with expertise in assaying phenotypes related to models of interest 5. Provide API hooks to use similarity algorithm to enhance Phenotips explanations of "you may wish to co-annotate this", based on both phenotypic profiles using HPO annotations and model systems phenotypic profiles. This is an indication of what differentiating phenotypes might be most important to record. 6. Make additional phenotype data and improved algorithm available via OWLSim 7. Integration of phenotypic similarity approach with PPI, co-expression, etc. to cover cases where an animal model does not yet exist but pheno-copying pathway partners do. 8. Improvement of HPO request pipeline. The Government will create a request service that would allow users to submit requested terms along with supporting material, including parentage, database cross-references, and PubMed IDs. The service will be based on software developed at LBL (termgenie.org) for use in the Gene Ontology and will be adapted for use with the Human Phenotype Ontology (HPO). We will refactor the HPO using the Web Ontology Language (OWL) in order to support this functionality. 9. Develop semantic models of temporal and severity characteristics to support Phenotips data entry. 10. Improved logical definitions for maximal interoperability with other organisms and data types. This could include improved annotations and terms for diseases of interest at UDP, coordination with mammalian phenotype ontology as needed. 11. The Contractor shall work with Ruro Inc. to test UDP-LIMs for data consistency and export: a. Data consistency risks; b. Ontology integration; c. Phenotype-genotype export functionality ; d. Data and software version control; e. Phenotips integration; f. Opportunities for enhancements surrounding workflow provenance and visualization; and g. Curation guidance. 12. Usability evaluation through static usability inspections, including heuristic evaluation and cognitive walkthrough, to identify possible usability concerns and to suggest appropriate interface revisions. 13. Analyze Phenotips entry with respect to HPO to identify HPO/other ontology needs/opportunities. 14. Work with UDP-LIMS to define general curation guidelines that can be leveraged in UDP-LIMS, Phenotips, and by UDP extramural sites for consistent and quality genotype-phenotype data export (no PII). 15. Aid Phenotips in implementing logical rules (e.g. things like checking for gender-specific phenotypes), and tooltips for the rest of the guidelines 16. Determine QA measures and consider mechanisms to measure inter and intra-annotator consistency given the few clinical annotators and disparate records 17. Create preliminary data exchange format standard for UDP genotype-phenotype data. B. Desired Results/Functions/End Items : 1. A web service API returning genes and models based on phenotype similarity, improved tools for HPO phenotyping, and full integration of tools into the UDP work flow (LIMS). 2. Research collaborations will be conducted via Videoconferences, email communications, shared professional presentations, posters and publications. Grand Round presentations at the Contractor's location and the NIH Clinical Center may also occur. C. Technical Specifications/Standards/Methods : 1. The Contractor shall develop and supply required algorithms, software tools to accomplish the above as well as assist in the implementation of these tools in the UDP work flow (LIMS). 2. The Contractor shall supply results with qualified interpretations in formats appropriate to the process management systems and for facilitation of other collaborations. D. Special Handling or Handling Requirements : 1. The Contractor shall provide result reports and record methods and materials as appropriate to the highest scientific standards. These materials, methods and results will be shared will agreed upon UDP collaborators. E. The Government will provide to the Contractor: 1. The Government will not furnish any government property to the vendor 2. The Government will provide the data for analysis of the effectiveness of the tools being developed; this include phenotypes and exome data. 3. The Government will not furnish any facilities to be used by the vendor. The Government will be responsible for reviewing and approving reports and similar matters generated: 1. Results will be provided electronically to the UDP via secure email, the UDP ftp site or direct deposition into the UDP process management system. 2. Results will also be shared with UDP collaborators as defined mutually. F. Reporting Requirements and Deliverables : 1. The Government will receive all electronic results, software and tools within 52 weeks of initiation of the contract, and the contractor will assist the UDP with integration of these into the UDP workflow (LIMS) within that timeframe. vi. NIH/UDP is located at 9 Memorial Drive, Bethesda, Maryland 20892. vii. The FAR Provision 52.212-1, Instructions to Offerors -- Commercial, applies to this acquisition and is hereby incorporated by reference. All Federal Acquisition Regulations (FAR) clauses may be viewed at http://acquisition.gov/comp/far/index.html. viii. EVALUATION OF PROPOSALS: The Government will evaluate proposals that are determined technically acceptable in accordance with the Technical Evaluation factors. The Government intends to award a single contract from this solicitation. The Government reserves the right not to award a contract. Evaluation of Proposals : The Government reserves the right to make an award without discussions based solely upon initial proposals. EVALUATION FACTORS : 1. Ability to map phenotype characteristics across multiple species if the human phenotype is curated in human phenotype ontology. 2. Ability to map phenotypes to researchers working on those phenotypes in humans or model organisms. 3. Ability to integrate the UDP phenotyping activity with improved curation of the human phenotype ontology database. 4. Ability to use UDP phenotyping activity to improve the UDP phenotyping tool (Phenotips). 5. Ability to provide constructive feedback on the UDP information and process management and communications system. 6. Ability to define curation and phenotyping guidelines to achieve optimal data entry and use. A. Price (This will be Firm-Fixed Price): An evaluation of the offeror's price proposal will be made to determine if proposed prices are realistic for the work to be performed, reflect a clear understanding of the requirements, and are consistent with the technical proposal. Reasonableness determinations will be made by determining if competition exists, by comparing proposed prices with established commercial or GSA price schedules (if applicable), and/or by comparing proposed prices with the Independent Government Cost Estimate (IGCE). ix. In accordance with FAR Clause 52.212-3, Offeror Representations and Certifications - Commercial Items, offerors must complete annual representations and certifications on-line at https://www.sam.gov/portal/public/SAM/. x. FAR clause 52.212-4, Contract Terms and Conditions - Commercial Items applies to this Acquisition. xi. FAR clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items applies to this Acquisition. xii. The Defense Priorities and Allocations System (DPAS) and assigned rating does not apply to this acquisition. Offerors shall submit their proposals no later than 7:30 a.m. Eastern Standard Time (EST) on July 9, 2013. The proposal must reference the RFP Number: NHLBI-CSB-(HG)-2013-199-DLM. All responsible offerors may submit a proposal, which if timely received, shall be considered by the agency. Proposals can be emailed to the Contracting Specialist, Dorothy Maxwell at maxwelld@nhlbi.nih.gov; Quotations shall not be deemed received by the Government until the quotation is entered into the e-mail address inbox set forth above. Faxed proposals will NOT be accepted. Offerors' proposals shall not be deemed received by the Government until the proposal is entered into the e-mail address inbox set forth above. All quotes shall contain the following: 1. Name of Contracting Organization; 2. Contract Number (for subcontracts, provide the prime contract number and the subcontract number); 3. Contract Type; 4. Total Contract Value and Discounts; 5. Description of Requirement; 6. Contracting Officer's Name and Telephone Number; 7. North American Industry Classification System (NAICS) Code; and 8. DUNS Number. Offerors must complete annual representations and certifications on-line at https://www.sam.gov/portal/public/SAM/.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-CSB-(HG)-2013-199-DLM/listing.html)
- Place of Performance
- Address: NIH, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Zip Code: 20892
- Record
- SN03105932-W 20130704/130702235434-9300ff5aa0e4fc63df3c56e85d7cfd68 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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