From af5b11e8b72581780fdf50e6230a9f1ec4f067ef Mon Sep 17 00:00:00 2001 From: Thomas Schaffter Date: Tue, 23 Feb 2021 08:32:23 -0800 Subject: [PATCH] Update date annotator description (#178) * Update date annotator description * Update description of the three annotators --- openapi/date-annotator/openapi.yaml | 44 ++++++++++++++++--- openapi/person-name-annotator/openapi.yaml | 41 ++++++++++++++--- .../physical-address-annotator/openapi.yaml | 43 +++++++++++++++--- 3 files changed, 112 insertions(+), 16 deletions(-) diff --git a/openapi/date-annotator/openapi.yaml b/openapi/date-annotator/openapi.yaml index 853f8afe..3df0ce2b 100644 --- a/openapi/date-annotator/openapi.yaml +++ b/openapi/date-annotator/openapi.yaml @@ -11,16 +11,48 @@ info: url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE x-logo: url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png - description: | - # Overview + description: > + # Introduction - This NLP tool detects references of dates in the clinical note given as - input and returns a list of date annotations. + The Date Annotator is one of the first type of NLP Tools that can be + benchmarked on [nlpsandbox.io]. A Date Annotator takes as input a clinical + note and outputs a list of predicted date annotations found in the clinical + note. This OpenAPI document describes the specification of a Date Annotator. + This specification includes the schemas of the input and output data, and + the conditions that this annotator must meet if you want to benchmark its + performance on [nlpsandbox.io]. + + # Getting Started + + The GitHub repository [nlpsandbox/date-annotator-example] provides a simple + example implementation of a Python-Flask Date Annotator. By the end of the + tutorial available in this repository, you will have built a Docker image + for a simple Date Annotator. You will then be able to submit this image to + [nlpsandbox.io] to benchmark its performance. + + # Benchmarking Requirements + + The following conditions must be met by your Date Annotator if you want to + benchmark its performance on [nlpsandbox.io]. + + - The endpoint `/` must redirect to `/api/v1/tool`. + - The endpoint `/ui` must redirect to the web interface (UI). + - The output of this tool must be reproducible: a given input should always + generate the same output. + - This tool must not attempt to connect to remote server for reproducibility, + robustness, and security reason. When benchmark on [nlpsandbox.io], this + tool will be prevented from connecting to remote servers. # Examples - - [NLP Sandbox Date Annotator (Python)](https://github.com/nlpsandbox/date-annotator-example) - - [NLP Sandbox Date Annotator (Java)](https://github.com/nlpsandbox/date-annotator-example-java) + - [Date Annotator Example (Python)] + - [Date Annotator Example (Java)] + + + [nlpsandbox.io]: https://nlpsandbox.io + [nlpsandbox/date-annotator-example]: https://github.com/nlpsandbox/date-annotator-example + [Date Annotator Example (Python)]: https://github.com/nlpsandbox/date-annotator-example + [Date Annotator Example (Java)]: https://github.com/nlpsandbox/date-annotator-example-java tags: - name: HealthCheck description: Operations about health checks diff --git a/openapi/person-name-annotator/openapi.yaml b/openapi/person-name-annotator/openapi.yaml index 816a7a2b..e584710f 100644 --- a/openapi/person-name-annotator/openapi.yaml +++ b/openapi/person-name-annotator/openapi.yaml @@ -11,15 +11,46 @@ info: url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE x-logo: url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png - description: | - # Overview + description: > + # Introduction - This NLP tool detects references of person names in the clinical note given - as input and returns a list of person name annotations. + The Person Name Annotator is one of the first type of NLP Tools that can be + benchmarked on [nlpsandbox.io]. A Person Name Annotator takes as input a + clinical note and outputs a list of predicted person name annotations found + in the clinical note. This OpenAPI document describes the specification of a + Person Name Annotator. This specification includes the schemas of the input + and output data, and the conditions that this annotator must meet if you + want to benchmark its performance on [nlpsandbox.io]. + + # Getting Started + + The GitHub repository [nlpsandbox/person-name-annotator-example] provides a + simple example implementation of a Python-Flask Person Name Annotator. By + the end of the tutorial available in this repository, you will have built a + Docker image for a simple Person Name Annotator. You will then be able to + submit this image to [nlpsandbox.io] to benchmark its performance. + + # Benchmarking Requirements + + The following conditions must be met by your Person Name Annotator if you + want to benchmark its performance on [nlpsandbox.io]. + + - The endpoint `/` must redirect to `/api/v1/tool`. + - The endpoint `/ui` must redirect to the web interface (UI). + - The output of this tool must be reproducible: a given input should always + generate the same output. + - This tool must not attempt to connect to remote server for reproducibility, + robustness, and security reason. When benchmark on [nlpsandbox.io], this + tool will be prevented from connecting to remote servers. # Examples - - [NLP Sandbox Person Name Annotator (Python)](https://github.com/nlpsandbox/person-name-annotator-example) + - [Person Name Annotator Example (Python)] + + + [nlpsandbox.io]: https://nlpsandbox.io + [nlpsandbox/person-name-annotator-example]: https://github.com/nlpsandbox/person-name-annotator-example + [Person Name Annotator Example (Python)]: https://github.com/nlpsandbox/person-name-annotator-example tags: - name: HealthCheck description: Operations about health checks diff --git a/openapi/physical-address-annotator/openapi.yaml b/openapi/physical-address-annotator/openapi.yaml index 453d3fa3..72fdf1a7 100644 --- a/openapi/physical-address-annotator/openapi.yaml +++ b/openapi/physical-address-annotator/openapi.yaml @@ -11,15 +11,48 @@ info: url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE x-logo: url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png - description: | - # Overview + description: > + # Introduction - This NLP tool detects references of physical addresses in the clinical note - given as input and returns a list of physical address annotations. + The Physical Address Annotator is one of the first type of NLP Tools that + can be benchmarked on [nlpsandbox.io]. A Physical Address Annotator takes as + input a clinical note and outputs a list of predicted physical address + annotations found in the clinical note. This OpenAPI document describes the + specification of a Physical Address Annotator. This specification includes + the schemas of the input and output data, and the conditions that this + annotator must meet if you want to benchmark its performance on + [nlpsandbox.io]. + + # Getting Started + + The GitHub repository [nlpsandbox/physical-address-annotator-example] + provides a simple example implementation of a Python-Flask Physical Address + Annotator. By the end of the tutorial available in this repository, you will + have built a Docker image for a simple Physical Address Annotator. You will + then be able to submit this image to [nlpsandbox.io] to benchmark its + performance. + + # Benchmarking Requirements + + The following conditions must be met by your Physical Address Annotator if + you want to benchmark its performance on [nlpsandbox.io]. + + - The endpoint `/` must redirect to `/api/v1/tool`. + - The endpoint `/ui` must redirect to the web interface (UI). + - The output of this tool must be reproducible: a given input should always + generate the same output. + - This tool must not attempt to connect to remote server for reproducibility, + robustness, and security reason. When benchmark on [nlpsandbox.io], this + tool will be prevented from connecting to remote servers. # Examples - - [NLP Sandbox Physical Address Annotator (Python)](https://github.com/nlpsandbox/physical-address-annotator-example) + - [Physical Address Annotator Example (Python)] + + + [nlpsandbox.io]: https://nlpsandbox.io + [nlpsandbox/physical-address-annotator-example]: https://github.com/nlpsandbox/physical-address-annotator-example + [Physical Address Annotator Example (Python)]: https://github.com/nlpsandbox/physical-address-annotator-example tags: - name: HealthCheck description: Operations about health checks