ESTminer

IntegratedMap

IntegratedSearch

OxfordGrid


Sharing of Results and Management of Intellectual Property

All data resulting from this award will be made freely available to the non-profit scientific community in a timely manner (see below), and will be made accessible to the public via Web-based resources. To ensure against loss of biological materials or distribution delays, all shared physical resources, such as DNA clones, will be maintained at a minimum of two locations (as described below), each of which will be able and authorized to respond to requests for distribution. The proposed work will yield comparative genetic and physical data, as well as DNA sequence and expression data that will be relevant to many major crops. Publications that describe the broad messages arising from these data will be promptly prepared for leading refereed journals. The vast majority of data, including the identities and arrangements of individual BAC clones, DNA sequences, etc, will not be appropriate for the published literature, but are of utmost importance for ongoing research in many taxa.

  1. Release of sequence and other community resources: All STC data will be deposited into the Genome Survey Sequence section (GSS) of Genbank within one month of sequence generation. The STC data (flat files, trace files and quality files) will also be made available at our ftp site (ftp.genome.clemson.edu). 'Re-sequencing' data from Cornell and UGA, including SSR, SNP, and candidate gene/promoter sequences, will be deposited in the same timeframe, and also maintained in the database. As of this writing, from the current funding period, 58,102 ESTs have been deposited in GenBank, all of which meet widely-used quality standards (Q16 on ABI3700, Phred 20 on ABI377). Comparable quality standards will continue to be used.

    Regarding physical map revisions, communication between FPC and the CSGR database will have an update component and a web display component. The update component consists of nightly cronjobs (NB at the Sanger Centre, FPC exchanges data with an Oracle database using this scenario). A cronjob will execute a batch FPC process to write a file of contigs and read a file of markers generated by the CSGR database. Another cronjob will execute a batch process to read the FPC generated file into the CSGR database and write the marker file. The files will be placed in directories that will be accessible by both databases.

  2. Fee structure for providing community resources; Mapped probes will be distributed in 96- well plates. EST clones and BACs will be distributed in 384-well plates. Arrayed libraries (or subsets thereof) in their original arrangement will be at a cost of $10 per (96- or 384-well) plate. If 'rearraying' or other sampling of a subset of clones is required for needs that are unique to one researcher (at our discretion), this will be at a cost of $5 per clone - in many cases it may be cheaper for a researcher simply to purchase the library and choose the clones themselves. However, in cases where re-arraying leads to a new set of plates that can be widely distributed, such as a tiling path for the sorghum genome, pricing will be initially be $25 per plate for the first 5 copies, falling to $10 per plate after that. High-density blots of the BAC libraries will be prepared on a cost-recovery basis fee (presently $125; compared to commercial rates of $350 or more) per 500 cm2 membrane containing 18,432 double-spotted clones. All rates are subject to reasonable adjustment at the discretion of the distributing unit, based on wage and price levels.


  3. Assurance of no reach-through rights on proprietary data used (if any); Various partners have reserved limited rights, as follows:
    • At present, the SUCEST sugarcane ESTs have not yet been deposited into Genbank, but are accessible after approval of a standard MTA (see scan following letter from Arruda). Our use of them is solely as informatic resources, to identify sorghum ESTs that are potential orphan genes. No reach-through rights convey.
    • Any patentable discoveries made in the course of ICSB-sponsored research are the property of the research provider (Dr Paterson/UGA or Dr Wing/Clemson, respectively). The ICSB will be granted a nonexclusive, nontransferable, royalty-free license to any invention or discovery conceived during the course of the research project. Acknowledgement of ICSB support is to be made in publications of the results of sponsored investigations.
    • Technology, inventions, and writings developed in the course of USGA-sponsored research to Dr.Paterson become the property of the University of Georgia. USGA reserves a non-exclusive, royalty-free, irrevocable worldwide license to use technology, inventions, and writings developed in the course of their sponsored research, and a 50% share of royalties (if any) resulting from such technology, inventions, or writings. Acknowledgement of USGA support is to be made in publications of the results of sponsored investigations.
    • Gene Indices that have been created for sorghum by TIGR may be a potentially valuable resource. However, inspection of the TIGR licensing agreement during the summer of 2000, first by individual scientists, and later by NSF personnel and Univ. GA legal counsel, raised questions about whether the agreement claims reach-through rights. After discussion with an NSF Plant Genome Program representative (J. Silverthorne), it was agreed that Univ. GA legal counsel (J. Butler) should further investigate this issue. This is in progress. Until a conclusion is reached, we will defer use of the TIGR Gene Indices, so as to eliminate the risk of any reach-through rights.

  4. Plan for short-term and long-term distribution of project outcomes. Responsibility for IP management lies with the lead institution. BAC libraries have been made, and are distributed and curated by the Wing (SB, rice, sugarcane) and Paterson (SP) labs. Each library is backed up at both locations, although the indicated location has distribution responsibility (requests should be directed accordingly). QBOTs are located at both locations. Cost structure is described above.

    Amplified cDNA libraries, and individual clones from which ESTs are derived were generated under the initial funding period, and may be requested under the commitments made at that time (from the Cordonnier-Pratt/Pratt lab). Backup copies are maintained at one or more of the other labs with interest in particular libraries.

    Clones will also be offered to the American Type Culture Collection; however in view of the large volumes of space that are occupied by our libraries (hundreds of plates per library), they have shown little interest in the past. Given our access to QBOTs, we feel comfortable serving as the primary distribution points.

    Long-term data access is provided by a Web-based resource, maintained at the University of Georgia. Matching support from UGA (Patel, Cherry letters) assures that there will be a network administrator to help co-PI Gingle with routine aspects of computational needs, and free Gingle to concentrate on programming. In addition, UGA underwrites the long-term maintenance of the online and functional status of the database (see letter from G. Patel). Stand-alone software tools developed under this support will be available to the non-profit research community for the purposes of academic research through free academic license agreements. Distribution will be through WWW download pages or via ftp.