PHIS Introduction 

10/25/21 

Introduction to the Public Health Information System 

The Food Safety and Inspection Service (FSIS) is the public health regulatory 

agency responsible for ensuring that domestic and imported meat, poultry, and 

processed egg products are safe, wholesome, and properly labeled. FSIS has 

made significant advances in the inspection process and is constantly evolving to 

enhance our ability to protect public health. Looking back, certain milestones may 

come to mind. In 1906, Congress passed the Federal Meat Inspection Act. In 

1996, FSIS finalized the “Pathogen Reduction: Hazard Analysis Critical Control 

Point (HACCP) Systems” rule. In 2011, FSIS implemented the Public Health 

Information System (PHIS) to support a data-driven approach to FSIS inspection, 

auditing, and scheduling. 

Objective 

To demonstrate mastery of this module, Inspection Program Personnel (IPP) will 

be able to explain how PHIS enhances inspection and protects public health. 

PHIS Introduction 

PHIS is a user friendly, web-based application that replaces several legacy 

systems and automates many processes. It allows FSIS to obtain and quickly 

analyze more data about domestic and international food safety systems 

producing FSIS regulated products. It also enables the Agency to better identify 

food safety risks before they result in outbreaks or recalls. The Predictive 

Analytics component supports a data driven approach to inspection and sampling 

by automatically searching data to identify trends and notifying FSIS personnel 

about potential public health threats. 

PHIS generates specific tasks and adjusts task frequencies based on public 

health risk factors. IPP, supervisors, and analysts access real time data for early 

recognition of food safety system deficiencies and trends. Data is used to quickly 

and effectively respond to prevent product adulteration, recalls, and outbreaks. 

The quality of the analysis and the response however depends on the quality of 

the data in the system. It is critical that IPP enter data that is complete and 

accurate. 

PHIS was developed in response to an Office of the Inspector General (OIG) 

recommendation that FSIS develop an integrated data infrastructure to support a 

comprehensive, timely and reliable data driven inspection system. PHIS enables 

FSIS to utilize real time data to inform all aspects of its business process (e.g. 

domestic inspection, import inspection, and export activities). 

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PHIS Introduction 

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PHIS replaced several legacy systems, facilitating maintenance and analysis of 

the composited data. Work efficiency and effectiveness continues to improve 

since FSIS personnel with different roles (e.g. inspectors, managers, analysts, 

policy developers) can readily access and utilize inspection and sampling data. 

Agency resources are better utilized since tasks are prioritized. 

There are four functional areas within PHIS: 

• Domestic Inspection 

• Exports Certification 

• Imports 

• Predictive Analytics 

This course covers Domestic Inspection and Export Certification. Imports are 

covered in a separate course. 

PHIS is role based. There are many different roles based on duties, job 

description and job series. Each user role sees a unique navigation menu. For 

example, CSIs can access establishment profile, task calendar, inspection 

verification data, animal disposition, and export certification menus for their 

assignments. 

Establishment profile data drives many important PHIS functions. Therefore, IPP 

must routinely update and ensure the accuracy of the profile data. The profile 

includes critical information about the establishments’ operations, product types, 

product volumes, and HACCP system. This information allows FSIS to tailor 

inspection, sampling, or other activities based on establishment factors. Sample 

requests are electronically routed to inspectors based on establishment profile 

information. If profile data is inaccurate or missing, IPP could receive sample 

requests for products that the establishment no longer produces. 

A “task list” is generated for each establishment based on profile data. The task 

list identifies task priorities and frequencies. IPP consider the task priorities, time 

constraints, and their knowledge of establishment operations to schedule tasks 

on their task calendar. 

In addition to routine tasks, “directed” tasks may be added to the task list. PHIS 

generates some directed tasks in response to sample results. Sample tasks 

specify a time frame during which IPP are to schedule and collect the requested 

sample. IPP can add directed tasks to document a noncompliance found when 

not performing a routine task. PHIS also allows directed tasks to be initiated at 

various Agency levels and targeted to subsets of establishments in response to 

public health findings or other information. The system tracks completion of tasks 

and can alert supervisors when tasks are performed. 

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PHIS Introduction 

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PHIS contains links to applicable guidance material (e.g., Directives, Notices). 

The guidance is based on the establishment profile and the specific inspection 

task. Linking to only the applicable guidance reduces time spent searching for 

and reviewing information that may not be helpful or pertinent. 

In PHIS, IPP document the specific regulations verified and the findings of 

compliance or noncompliance for each regulation. If a noncompliance is found, it 

is documented on an NR along with other applicable information such as product 

type, lot number, retain or reject tags used, and/or the applicable CCP verified for 

some tasks. The system also facilitates documenting meeting minutes in a 

memorandum of interview (MOI). Inspectors can create notes in PHIS that can 

be used to communicate with other inspectors or included as agenda topics for 

meetings. 

FSIS began implementing the PHIS Export Component on June 29, 2018, with a 

limited number of 16 countries, and then gradually expand to additional 

countries. Phase one includes Afghanistan, Andorra, Bahamas, Bolivia, Burundi, 

Cape Verde, Cook Islands, Ethiopia, French Guiana, Gambia, Guinea, Liberia, 

Mozambique, San Marino, Tanzania and Uganda. Additional countries have 

since been added and will continue to be added. Please see FSIS Notices for 

additional information. 

For active countries in PHIS Export module, applicants must submit an 

application through PHIS or submit a paper application for the contractor to enter 

it into PHIS. PHIS will verify the eligibility of the product based on Hazard 

Analysis and Critical Control Points (HACCP) category, species, and maturity (for 

beef only). Once PHIS validates the application, an export task is generated in 

the establishment task list on the task calendar. The export task name will 

contain the seven (7) digit export application number that is generated by PHIS. 

PHIS will generate a separate export task for each submitted export application. 

IPP should perform the Export Task and provide the applicant with the export 

certificate printed on a security paper. 

You can access information about Country Rollout Schedule, Information for 

Industry, Information for Foreign Governments and FSIS Inspection Program 

Personnel, and Rulemaking/Reference Documents on the FSIS website 

https://www.fsis.usda.gov/inspection/import-export/phis-components. We will 

discuss export more in detail on week 2 of this training course. 

PHIS will manage export applications, export certificates, and product eligibility. 

The Application for Export Certificate and the Export Library provide the data 

necessary for PHIS to populate the entire export certificate. The export 

certificate is validated by the Export Library Validation Service eliminating the 

need for an attached AMS Statement of Verification and manual verification of 

establishment and product eligibility. Inspectors only verify those requirements 

not checked by the Export Library Validation Service. They approve the export 

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PHIS Introduction 

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application, conduct reinspection, and permit the establishment to stamp the 

product; but they do not have to issue a certificate to the applicant for completion 

because PHIS completes the certificate. The inspector’s signature is an 

electronic signature for those countries that receive electronic certificates. 

Inspectors or PHVs do not have to review the official export certificate unless the 

country requires a signed hard copy. Likewise, inspectors or PHVs do not have 

to sign a final certificate, distribute the copies, or file official copies of the 

certificate if the importing country chooses to receive the certificate electronically. 

For replacement certificates, inspectors only review the material changes. The 

applicant is charged a fee for each application, and inspectors charge for 

reimbursable services in certain situations. 

Predictive Analytics 

Predictive analytics integrates data from various sources such as Centers for 

Disease Control, PulseNet, the Agricultural Research Service VetNet and the 

National Antimicrobial Resistance Monitoring System and stores the collected 

data in the FSIS Data Warehouse. Algorithms perform real time data analysis. 

When anomalies are identified, PHIS sends alerts to the appropriate user 

homepages or email addresses. Users may subscribe to alerts that are of 

interest. 

Predictive analytics also uses algorithms to automate scheduling in response to 

certain events. The system generates appropriate follow-up tasks in response to 

sampling results. For performing and scheduling directed tasks, IPP should 

follow guidance in FSIS Directive 13,000.1. 

Predictive analytics incorporates decision criteria to schedule Food Safety 

Assessments and identifies when an establishment should reassess their hazard 

analysis. Analysts can also conduct spontaneous data analyses from multiple 

data sources to identify trends and anomalies. 

Predictive analytics has data reporting and visualization tools. The system can 

flag unusual events within reports and bring them to the attention of FSIS 

personnel. The reporting functionality allows users to drill-down to underlying 

data, populating the report and flag anomalies. Visualization tools include box 

plots, trend lines, maps, etc., in addition to standard tables. 

This introduction is a brief overview of how PHIS improves our inspection system 

to better protect public health. Policy modules, hands-on computer training, and 

workshops will follow. 

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