diff --git a/docs/source/design/concepts/index.rst b/docs/source/design/concepts/index.rst new file mode 100644 index 00000000..39250555 --- /dev/null +++ b/docs/source/design/concepts/index.rst @@ -0,0 +1,16 @@ +.. _about_concepts: + +============== +Concept Schema +============== + +A key part of the ingest library is the intermediate model of the +"concept schema". This concept schema is a representation of the data that is +being ingested, and is used to generate the final schema that is used to create +the tables in the target api. + + +.. toctree:: + :maxdepth: 2 + + samples_and_specimens.rst diff --git a/docs/source/design/concepts/samples_and_specimens.rst b/docs/source/design/concepts/samples_and_specimens.rst new file mode 100644 index 00000000..129084be --- /dev/null +++ b/docs/source/design/concepts/samples_and_specimens.rst @@ -0,0 +1,30 @@ +===================== +Samples and Biospecimens +===================== + +Although similarly named, samples and biospecimens refer to different things: + +- A **sample** is a physical piece of tissue, blood, or other material taken +from a patient. +- A **biospecimen** is a part of that sample, e.g. an aliquot of a sample. + +While samples and biospecimens are distinct concepts, they share much in common. +In fact, when the ingest library was first written, its primary target API, +the Kids First Data Service, only had a table for biospecimens. As a result, +the ingest library's architecture provides for a biospecimen to share *all* the +qualities of a sample. In fact, biospecimen is a child class of sample! + +This architecture allows the ingest library to be used against target APIs that, +like the older versions of the Kids First Data Service, only have a table for +biospecimens. + +A sample has qualities: + +* A sample may have ino + +A biospecimen takes on +This +is the smallest unit that a piece of biological material can take, as +represented in the ingest library. + +Some \ No newline at end of file diff --git a/docs/source/design/overview.rst b/docs/source/design/overview.rst index d3cc1536..2cbd4e13 100644 --- a/docs/source/design/overview.rst +++ b/docs/source/design/overview.rst @@ -40,6 +40,7 @@ described. :maxdepth: 1 value_principles + concepts/index.rst extract_mapping transform load