Add draft pedigree model

model.md

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+# Pedigree conceptual model
+
+## Motivation
+
+Lack of interoperability of pedigree data between systems results in a substantial double-entry burden for already-overloaded nurses, genetic counselors, and support staff, and introduces the potential for serious errors.
+
+# Classes
+
+![image](https://user-images.githubusercontent.com/4251264/105409205-1c53b200-5bfe-11eb-9d77-ed5630138eaf.png)
+
+## Pedigree
+
+A `Pedigree` is collection of selected information about a family, including the individuals, relationships between them, and relevant health conditions.
+
+### properties
+
+| Field | Type | Status | Definition |
+| --- | --- | --- | --- |
+| proband | ID | optional | id of Individual that is the index case for the family |
+| consultand | ID | optional | id of Individual that is the focus of the current analysis |
+| date | Date | optional | the date the pedigree was collected or last updated, as ISO full or partial date, i.e. YYYY, YYYY-MM, or YYYY-MM-DD |
+| reason | Concept | optional | the reason for pedigree collection, especially a health condition of focus being investigated in the family; if any Individual has the `affected` property defined, it refers to this condition |
+
+## Individual
+
+### properties
+
+| Field | Type | Status | Definition |
+| --- | --- | --- | --- |
+| id | ID | required | logical id |
+| name | string | optional | name of the individual |
+| identifiers | list of string | optional | external identifiers for the individual |
+| sex | Concept | required | Sex assigned at birth, values: `male`, `female`, `other`, `unknown`; See: https://confluence.hl7.org/display/VOC/Gender+Harmony+Context+Definitions and https://www.hl7.org/fhir/valueset-administrative-gender.html |
+| gender | Concept | optional | Presumed or reported gender identity, values: `male`, `female`, `non-binary`, `non-disclosed`, `trans`, ...; See: https://confluence.hl7.org/display/VOC/Gender+Harmony+Context+Definitions |
+| lifeStatus | Concept | recommended | The presumed/accepted life status of the individual as of the pedigree collection date; one of: `alive`, `deceased`, `unborn` |
+| affected | boolean | not recommended | whether or not the individual is affected by the condition being investigated in this pedigree; included for PED backwards compatibility |
+
+## Relationship
+
+### properties
+| Field | Type | Status | Definition |
+| --- | --- | --- | --- |
+| id | ID | required | logical id |
+| individual | ID | required | identifier of the subject Individual; equivalent to the FHIR "Scoping Individual" and the Biolink "Subject" |
+| relation | Concept | required | the relationship the `relative` has to the `individual` (e.g., if the `relative` is the `individual`'s parent, then relation would be Parent); terms should come from the relationship terminology, linked below |
+| relative | ID | required | identifier of the relative Individual; equivalent to the FHIR "Player" and the Biolink "Object" |
+
+
+## Relationship Terminology
+
+See: https://docs.google.com/spreadsheets/d/1V5i-pbOPgg9_F52lYkQpqYbk3u4MIAc9TNw8aglvLL4/edit?usp=sharing
+
+## Implementation guidance
+Properties to link instances of the classes are intentionally omitted in order to make the model agnostic to either a tabular or a hierarchical representation.
+
+
+# Supporting formats
+
+## ID
+This is a **string** identifier for internal cross-referencing of individuals between the components of a Pedigree.
+
+## Concept
+For simplicity, this is just a string URI/CURIE
+
+# TODO
+- add Event class for collecting birth, death, conditions, and attribution/provenance for this data
+- linking with other terminologies:
+  - request that ECO add new term, subclass of ECO_0006151, for family-member assertion (versus self-reported), to distinguish ECO:0006154, in which a patient is giving a statement about themselves, or sibling of ECO_0006153 since it's not self-reported, it's from a family member, for now, can use ECO:0006151 for it
+  - request that Biolink add a IndividualOrganismToIndividualOrganismAssociation class
+  - request that Phenopacket Disease allow status to represent carrier/asymptomatic/presymptomatic