Progress 06/01/12 to 05/31/16
Outputs
Target Audience:The primary target audience consists of the diagnosticians associated with the Land Grant Universities and state departments of agriculture, state plant regulatory officials, the NPDN Executive Team and the USDA/NIFA program leader and assosicate members of APHIS. In addition, the first detectors, extension staff and other associates of plant diagnostic labs are targeted through the newsletters and regional websitesof the NPDN portals, which also provide general information about the NPDN network and its programsto the public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Presentations have been a means to communicate and interact with users about the NPDN National Repository and the portals, but also were an excellent professional deveopment opportunity. Both the director of CERIS and the Associate Director of the National Repository attended the NCPDN regional meetings each year in April 2013- April 2016 giving presentations on yearly national IT accomplishments and overall efforts in priortizing tasks. The Director has attended the APS meetings in 2012 - 2015 giving a presentation at the town hall meetings on recent accomplishments and future developments. Two key NPDN staff presented posters at the NPDN National Meeting in March 2016 titled, 'NPDN National Database Program Are committee:Assuring quality and Standard in NPDN Diagnostics Data' and "IT Committee: The NPDN Wouldnt' be Possible Without IT'. How have the results been disseminated to communities of interest?Users have continued to have a wide array of reports and map capabilities available when accessing the system. The NPDN First Submission by State Report, a pro-active means of communication which emailsthe first time a pest or pathogen is reported in a state to the appropriate audience,has been in operation during this time period. Modifications, based on user input, included the state where the sample came from and a description of the lab doing the diagnosis to better aid those receiving the reports. The hosting of the IT/Diagnosticians meeting in 2015, afterseveral years of no meeting due to financial resources, brought the diagnosticians and NPDN IT support staff together to understand, strategize and prioritize actions that expand and improve the IT resources for the diagnosticians, allowing the diagnosticians to focus on diagnostics. For those new to the network, an individualized webinar is provided as well as customer support via phone calls and emails for both data entry and access of reports. For the STAR-D effort Purdue provided technical assistance in the STAR-D accreditation webinars/conference calls. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The main accomplishments under these goals from 6/1/12 - 5/31/16 were - The move of the National Repository from the legacy Alpha system to a distributed virtualized environment using open source technologies with dedicated web, map and database servers. This move made innovative techonologies available for development, requiredfewer maintenance resources and provided better response time. In addition,a new featureincluded removing the requirement oftwo separateusernames and passwords for the National Repository and NPDN portal sitesbyincorporating one username and passwordfor both systems,thus simplifying the access process for the users. Additional enhancements that were released included adding a session timeout of 4 hours on the production site, updating pagination links to be compatible with IE7, updating software for Excel spreadsheets to allow up to 100,00 rows, rewriting of the selectable fields report software and updating the summary and selectable fields reports to retain previous search criteria. The continued growth of the the number of diagnosticrecords. Each year the number of records increased with the total number of diagnoses reaching the million recordmilestone in 2015. 6/1/12 - 5/31/13 - 93,176 6/1/13 - 5/31/14 - 97,187 6/1/14 - 5/31/15 - 183,393 6/1/15 - 5/31/16 - 204,591 Another new feature was the home page of the NPDN National Repository showing the summary statistics on diagnoses, pests, hosts, counties and diagnostic labs. As of May 31, 2016, there were over 1.27 million diagnoses covering over 11,600 unique pests or pathogens on over 3,400 hosts, in over 3,100 counties and from over 170 labs. Improved access of NPDN National Repository - In working with the NPDN Executive Committee to streamline the process for those requesting information on non-sensitive or non-confidential pests or pathogens, an iterative process took place which first provided regional access to all diagnosticians and some diagnosticians being granted national access as approved by their regional directors. With more individuals having national access, an electronic acknowledgement on the use of the data appears that must be agreed to before accessing the information, indicating the responsibility required. The Terms of Use statement that users must agree to with each session is - Permission to access data in the NPDN Data Repository does not confer rights to share, present, or publish any raw, processed or summary data from the NPDN Data Repository. Specific permission is required for each disclosure event whether digital or analog, oral or written and can be granted only by the NPDN Executive Committee. Ease of Uploading Data - One of the fundamental goals is for the ease of uploading data. With resource availability an issue, the California Department of Food and Agriculture diagnostic lab had some issues in transferring data and in the spring of 2015 a collaborative effort took place between UC Davis and Purdue resulting in over 75,000 confirmed diagnoses uploaded. Improvements in Pest and Host Dictionaries - The NPDN pest and host dictionaries, a valuable resouce used by other systems such as the Caps Information Services program, are easily accessible to LIMS systems, updated frequently for standardizationand reviewed by the NPDN Database Committee.From 6/1/12 - 5/31/16 there were 1,892 additions, 1,909 modifications and 70 deletions to the pest dictionary and 380 additions, 521 modifications and 3 deletions to the host dictionary.Purdue leads this effort in researching standard taxonomic names and entering the modifications andcollaborating with the Database Committee for additonal review on use and content expertise. A useful feature to the diagnosticians was the incorporation of synonyms which requirednew database design, structure and interface software to indicate the standard names while allowing searches on'older' naming conventionsand providing the means to become acquainted with the new standards. Improvement of NPDN Portal www.npdn.org - The regional sites, nepdn.org, sepdn.org, ncpdn.org, gpdn.org and wpdn.org, during the Drupal upgrade which included a new responsive design and innovative features,were all merged as one Drupal (open source software) site resulting in reduced maintenance resources. STAR-D Accreditation - With STAR-D accreditation becoming more important as a quality management certification for the diagnostic labs, a role based access Lab Accreditation section has been added to the NPDN portal. This area contains a wide variety ofinformation resourcessuch as presentations, technical requirements, management requirements, example laboratory protocols, meeting and conference call minutes, activities, archived documents and AAVLD accreditation symposium documents.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
The National Plant Diagnostic Network: Partnering to Protect Plant Systems , Plant Disease, James Stack, Richard M. Bostock, Raymond Hammerschmidt, Jeffrey B. Jones, Eileen Luke, 2014
Volume 98 Issue Number 6 pages 708-715
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Progress 06/01/14 to 05/31/15
Outputs
Target Audience: The primary target audience consists of the diagnosticians associated with the Land Grant Universities and state departments of agriculture, state plant regulatory officials, the NPDN Executive Team and the USDA/NIFA program leaders and associate members of APHIS. In addition, the first detectors, extension staff, and other associates are targeted through the newsletters, first detector training and general information of the NPDN portals. The portals also provide general information and newsletters about the NPDN to the public.The web statistics indicate over58,000 unique visitors for the national web portal, over 10,000 unique visitors for the GPDN portal, over 4,000 unique visitors for the NCPDN portal, over 15,000 unique visitors for the NEPDN portal, over 12,000 unique visitors for the SEPDN portal, and over 15,000 unique visitors for WPDN portal. Changes/Problems: There are no anticipated major problems to the general approach or plan in meeting the coming year's goals. One significant change is that the IT/Diagnosticians meeting whichhas not convened for five years will be held at Purdue. This is a critical componentbecause the interaction andfeedback are important for strategic planning and a sustained program. What opportunities for training and professional development has the project provided? CERIS staff again attended the North Central Plant Diagnostic regional meeting in April, 2015 which provided useful professional interaction and a better understanding of the diagnosticians' challenges and needs.A presentation was given on updates of the National Repository and upcoming developments. As was the case last year, CERIS staff attended two security symposiums and workshops - Center for Education and Research in Information and Assurance Security (CERIAS) at Purdue University and one in Indianapolis. These security symposiums have made staff more knowledgable in current security issues and have provided the means tomaintain their CISSP professional certifications. Such knowledge is invaluable in applications software development. How have the results been disseminated to communities of interest? Results have been disseminated through the National Repository by implementing reports and queries as suggested by the diagnosticains,giving presentations at the APS/NPDN Town Hall meeting, announcing new features and providing assistance on use of the National repository through newsletter articles, and participating at the NCPDN regional meeting with a presentation on updates to the National Repository. Also, the diagnosticians use the Pest Category Report and Lab Method Report available in the National Repository in their yearly accomplishments reports. What do you plan to do during the next reporting period to accomplish the goals? The goal of IT in the NPDN network is to provide with the highest level of customer support the most reliable, secure, and efficient information services to the diagnosticians and the NPDN network. The most significant new activity will be the IT/Diagnosticians meeting to be held on October 28-29, 2015 at Purdue University. The prioritized activities for Purdue University will continue to be the information flow to the NPDN National Repository, securing the information, and providing the information via web interface, reports and maps in a secure manner to appropriate parties. The quality of the data is critical so there will continue to be an allocated effort to work with the NPDN Database Committee in the standardization of the Pest and Host dictionaries and to review and assist in failed uploaded records. In particular, efforts will be made to reach out to diagnostic labs which may have appeared to provide fewer diagnostic records, discuss with the diagnostic lab and regional director the cause and see if some assistance can be provided. The Repository has become a useful and robust set of data, and every effort will be made to accommodate appropriate access and respond to requested subsets of data in a timely and efficient manner as approved by the NPDN Executive Directors. Communication between the IT staff and diagnosticians has provided sustained success and thus all efforts via phone calls, emails, conference calls, webinars, etc. will continue to be pursued in order to maintain a robust information service. These methods of communication will be utilized for the preparation of the IT/Diagnosticians meeting in October. Efforts will be made to attend regional meetings if held, attend society meetings such as APS which are heavily attended by the diagnosticians and attend the NPDN National meeting in March 2016. Behind the scene upgrades for both operating systems and applications will be done in a seamless manner to minimize risk of reduced or failed access. Critical Activities - The efforts that are most vital for the information flow of data into the National Repository and the access of information from the National Repository include, but are not limited to - Reviewing data upload issues and resolving issues with the diagnostician, industry participant, or individual responsible for data entry. Ensuring the first in state alert reports are processing and responding to all inquiries from the diagnosticians, National Program Leaders, and Executive Team members as quickly as possible. Assisting in the creation of key reports such as the Pest Category report to aid diagnosticians in their required metric reporting. Generating and presenting usage statistics for easy access and anlysis. Collaborating and reviewing pest and host standardized names as requested by the diagnosticians with the NPDN National Database Committee. Responding to users of the NPDN National Repository with the highest possible level of customer support. Assisting the National Program Leaders and Executive Team on special data requests and/or assistance in using the system.
Impacts
What was accomplished under these goals?
The main focus has continued to be the security, reliability and availability of the NPDN National Repository. The California Department of Food and Agriculture (CDFA) diagnostic lab had somechallenges inuploading data and in the last part of this cooperative agreement significant collaborative work has taken place with over 75,000 confirmed diagnoses uploaded. The National Repository also has industry data from 2007 - present with over 55,000 records from 39 states in which over 30,000 are confirmed samples. Over 170 diagnostic labs have uploaded to the repository since its inception with over 11,000 unique pests or pathogens, 3,800 unique hosts, and over 3,100 unique locations (counties). A major milestone has been reached in this cooperative agreement period with the National Repository now containing over 1 million diagnoses. From June 1, 2014 through May 28, 2015 over 180,000 records have been entered. A new feature of the NPDN Repository is the inclusion of synonyms in the Pest Dictionary. During the period June 1, 2014 - May 29, 2015, there were 1,119 adds(218 last year), 64 deletions (1 deletion last year) and 1,017 modifications (327 last year) to the NPDN Master Pest Dictionary. The larger than ususal number of additions and changes was due to the incorporation of the naming convention of fungi under the International Code of Nomenclature (ICN) for algea, fungi and plants. A user can now search on synonym names allowing familiarity with historically correct names and easily incorporating the standard scientific name in the output providing a means for the diagnosticians to master the new naming convention withlittleinconvenience. This change in the database design and software interface will allow for the use of synonyms as pest or pathogen namesare reviewed by the NPDN Database Committee in the future. Enhancements continued with the Pest Threshold report, which displays a listing of pest records based on sample date and threshold levels. The line chart featue using a scatter graph was implemented into production which included criteria of sample date range, pest, pest confidence level and line color. Support has continued with conference calls and webinars for the STAR-D accreditation review process allowing diagnosticians and associated staff to focus on diagnostics, their number one priority. Also, Beltsville training data has continued to be entered into the repository with summary reports available through the web interface with role based security access.
Publications
|
Progress 06/01/13 to 05/31/14
Outputs
Target Audience: The primary target audience consists of the diagnosticians associated with the Land Grant Universities and state departments of agriculture, state plant regulatory officials, the NPDN Executive Team and the USDA/NIFA program leaders and associate members of APHIS. In addition, the first detectors, extension staff, and other associates are targeted through the newsletters, first detector training and general information of the NPDN portals. The portals also provide general information and newsletters about the NPDN to the public. The web statistics indicate over51,000 unique vistors for the national web portal, over 7,000 unique visitors for the GPDN portal, over3,000 unique visitors for the NCPDN portal, over13,000 unique visitors for the NEPDN portal, over 10,000 uniques visitors for the SEPDN portal and over 14,000 visitors for the WPDN portal. Changes/Problems: There are no anticipated major changes/problems to the general approach or plan in meeting the coming year's goals. What opportunities for training and professional development has the project provided? The IT staff at Purdue University attended the North Central Plant Diagnostic regional meeting in April, 2014which provided useful professional interaction and a better understanding of the diagnosticians' challenges and needs. A presentation was given on the National Repository and included such items as website refresher, pest dictionary updates, Pest Threshold Report and Accomplishment Summary Reports. The presentation then guided discussion and feedback from the diagnosticians at the meeting. Collaborations and face to face discussionshave also taken place with the diagnosticians at Purdue who have provided guidance and advice on future enhancements and concerns about possible misinterpretations of the National Repository data. Two security symposiums and workshops were attended by staff - CERIAS (Center for Education and Research in Information and Assurance Security)symposium at Purdue University and one in Indianapolis. How have the results been disseminated to communities of interest? Results have been disseminated through the National Repository by implementing reports and queries as suggested by the diagnosticians, making presentations at the APS/NPDN Town Hall meeting, announcements of new features and assistance of use of the National Repository through newsletter articles, and participation at the Northeast Sentinel PlantNetwork meeting in January 2014.The NPDN portal has also provided a supportive role in STAR-D accreditation information with this section providing a wide variety of documents covering such topics as technical requirements, example laboratory protocols, meeting and conference call minutes, activities, archived documents, etc. In addtion, the diagnosticians use the Pest Category Report and Lab Method Report available in the National Repository in their yearly accomplsihments reports. What do you plan to do during the next reporting period to accomplish the goals? The goal of IT in the NPDN network is to provide with the highest level of customer support the most reliable, secure, and efficient information services to the diagnosticians and the NPDN network. The prioritized activities will continue to be the information flow to the NPDN National Repository, securing the information and providing the information via web interface, reports, and maps in a secure manner to appropriate parties in the most effective manner. The quality of the data is critical so there will continue to be an allocated effort to work with the NPDN Database Committee in the standardization of the Pest and Host dictionaries and the review and assistance in failed uploaded records. In particular, efforts will be made to reach out to diagnostic labs which may have appeared to provide fewer diagnostic records and discuss with the diagnostic lab and regional director the cause and see if some assistance can be provided. Enhancements or additions, such as the Pest Threshold Report with graphic enhancements, require efforts in communicating the use of these reports and in obtaining feedback. The Repository has become a useful and robust set of data andstaff will accommodate appropriate access and respond to requested subsets of data in a timely and efficient manner as approved by the NPDN Executive Directors. Communication between the IT staff and diagnosticians has provided sustained success via phone calls, emails, conference calls, webinars, etc. and will continue to be pursued in order to to maintain a robust information service.Every effort will be made to attend regional meetings if held and to host an IT/Diagnosticians meeting. Finally, all upgrades for both operating systems and applications will be done in a seamless manner with a major system upgrade planned for the mapping server. Critical Activities – These are the efforts that are most vital for the information flow of data into the National Repository and the access of information from the National Repository. These include, but are not limited to - Reviewing data upload issues, and resolving issues with the regional center, diagnostician, industry participant, etc. Ensuring that the first in state alert reports are processing and responding to all inquiries from the diagnosticians, National Program Leaders, Executive Team members, etc. as quickly as possible. Assisting in the generation of key reports such as the Pest Category report to aid diagnosticians in their required metrics reporting. Generating and presenting web statistics for easy access and analysis. Collaborating and reviewing pest and host standardized names as requested by the diagnosticians with the NPDN National Database Committee. Assisting the National Program Leaders and Executive Team on special data requests and/or assistance in using the system. Responding to users of the NPDN National Repository with the highest possible level of customer support.
Impacts
What was accomplished under these goals?
The main focus has continued to be the security, reliability and availability of the NPDN National Repository. Working with the Executive Committee in streamlining the process for those requesting information on non-sensitive or non-confidential pests or pathogens has resulted in an efficient and timely response for those requesting the information. In addition, diagnosticians have been granted regional access and a few diagnosticians from each regionhave been granted national access as approved by their regional directors making this robust data set more widely available to the diagnosticians. The National Repository has 872,819 records as of May 31, 2014from over 160 diagnostic labs with over 10,000 unique pests or pathogens, 3,200 unique hosts and over 3,100 unique locations. (counties) Industry data from 2007 - present comprises over 47,000 records from 39 states in which over 25,000 are confirmed samples demonstrating the greater participation and collaboration within the network. Over 96,000 new sample records were enterd from 6/1/13 - 5/31/14 With over 17,000 pests or pathogens in the NPDN Master Pest list, naming conventions have continued to be reviewed by the NPDN Database Committee. During the period June 1, 2013 – May 31, 2014, there were218 additions (177 last year), 1 deletion (1 last year), and 327 modifications (311 last year) to the NPDN Master Pest dictionary. During the same period, there were 111 additions (108 last year), 1 deletion (1 last year), and 48 modifications (48 last year) to the NPDN Master Host dictionary. Significant enhancements were the development and implementation of the Pest Threshold report, which displays a listing of pest records based on sample date and threshold levels and the addition of the state based pest/pathogen maps. With the focus of the network on diagnostics, support has been provided in lab accreditation. Conference and webinar support was provided during the accreditation review conference calls in order to allow the diagnosticians and associated staff the ability to focus on diagnostics and not be unduly burdened by IT logistics. In addition, Beltsville training data has been entered into the repository with summary reports available through the web interface with role based security access.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
The National Plant Diagnostic Network: Partnering to Protect Plant Systems
Plant Disease/Vol 98 No. 6
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Progress 06/01/12 to 05/31/13
Outputs
Target Audience: The primary target audience consists of the diagnosticians associated with the Land Grant Universities andstate departments of agriculture, the NPDN Executive Team and the USDA/NIFA program leaders and associate members of APHIS. In addition, the first detectors, extension staff, and other associates are targeted through the newsletters, first detector training, and general information of the NPDN portals. The portals also provide general information and newsletters about the NPDN to the public. The web statistics indicate over 28,000 unique visitors for the national web portal, over 5,000 unique visitors for the GPDN portal, over 3,000 unique visitors for the NCPDN portal, over 8,000 unique visitors for the NEPDN portal, over 9,000 unique visitors for the SEPDN portal and over 10,000 unique visitors for the WPDN portal. Changes/Problems: The move to the new operating system and associated applications software will provide a more robust computing environment allowingavailability of keysoftware development tools. The virtual machine environemnt has provided redundancy and backup at a reduced cost with new technologies of recovery available in a shorter time period. In addition, a more efficient and cost effective environment has helped to address the reduced funding situation. What opportunities for training and professional development has the project provided? The IT staff at Purdue University have attended regional diagnostician meetings and participated in webinars. Demonstrating the use of the system and acquiring a better understanding of the subject matter have been an excellent opportunity for professional development. How have the results been disseminated to communities of interest? Results have been disseminated through the National Repository by implementing reports and queries as suggested by the diagnosticians. The first in state submission report is a distributed report indicating the first occurrence of a pest/pathogen for a state not requiring the diagnosticians to have to pro-actively login to the system. The NPDN national portal has provided a supportive role in STAR-D Accreditation byoffering a role based access Lab Accreditation section which uses the content management system. This area contains presentations, a wide variety of documents such as technical requirements, management requirements, example laboratory protocols, meeting and conference call minutes, activities, archived documents and AAVLD accreditation symposium documents. What do you plan to do during the next reporting period to accomplish the goals? The prioritized activities for Purdue University will be the information flow to the NPDN National Repository, securing the information, and providing the information via web interface, reports and maps in a secure manner to appropriate parties in the most efficient manner. The quality of the data is critical so there will be an allocated effort to work with the NPDN database committee in the standardization of the Pest and Host dictionaries and the review and assistance in failed uploaded records. The conversion of the NPDN National Repository in January 2013 has provided an environment with faster response and better software development tools. The NPDN portals have been set up using open source technology and the total effort for maintaining the servers and associated software is at an optimal level. However, the main issue of support is in the content update and with the reduced staffing in the network, it is anticipated that the content management support will be at a lower maintenance level. Purdue will provide assistance here as resources allow. Purdue will also work with the NPDN Executive Team to administer data sharing requests and provide the information along with the understanding of how the data can be shared as requested noting that response can be diminished due to resources available. Communication between the IT staff and diagnosticians has provided sustained success and thus all efforts via phone calls, emails, conference calls, webinars, etc. will continue to be pursued in order to maintain a robust information service. Upgrades for both operating systems and applications will be done in a seamless manner and a significant effort will be required for mapping upgrades.
Impacts
What was accomplished under these goals?
The move of the National Repository from the legacy Alpha system to the virtual server with the MySQL database was completed on January 1, 2013. A significant change on the new site was that the username and password changed and became the same as the username and password that one uses to access the NPDN portal sites providing a less complicated means of access while maintaining the necessary security. The movewas the most significant software enhancement. Overall, it was noted that the system had a faster response. Some additional enhancements were released in the early months of 2013 which included adding a session timeout of 4 hours on the production site, updating pagination links to be compatible with IE7, updating software for Excel spreadsheets to allow up to 100,000 rows, rewriting of the selectable fields report software and updating the summary and selectable fields reports to retain previous search criteria. The NPDN First Submission by State Report was modified to include the state where the sample came from and a description of the lab doing the diagnosis to better aid those receiving these reports and having better information when further investigation is required for quality control and anomaly assessment. NPDN Master Pest and Host Lists - With over 17,000 pests or pathogens in the NPDN Master Pest list, naming conventions have continued, but there has been a slight reduction in overall changes indicating a more robust pest and host list. The list has continued to be a “work in progress” with the National Database Committee doing reviews of groups of pests. During the period 6/1/12 – 5/15/13, there were 311 additions (252 last year), 4 deletions (14 last year), and 348 modifications (233 last year) to the NPDN Master Pest dictionary. During the same period, there were 105 additions (164 last year), 0 deletions (2 last year), and 47 modifications (23 last year) to the NPDN Master Host dictionary indicating the list is in more of a ‘maintenance’ mode. Industry has participated in the NPDN with over 38,000 records from 38 states in which over 21,000 are confirmed samples since 2007. This also demonstrates the greater participation and collaboration within the network.
Publications
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