using wiki

README.md

@@ -3,118 +3,9 @@
 
 The health of an individual organism results from a complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient symptoms and disease features) and environmental factors (Figure 1). Phenotypic abnormalities of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, and even social media. However, the lack of standardization, accessibility, and computability among these contexts makes it extremely difficult to effectively extract and utilize these data, hindering the understanding of genetic and environmental contributions to disease. 
 
-For more information, start with [requirements.md](requirements.md)
+## Documentation
 
-## Walk-through example
+See the [Wiki](https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started) for documentation
 
 
-Phenopackets can be encoded in either JSON or YAML, there is no
-difference between the two. We will use YAML here for compactness.
 
-Our example involves a case study with three people (phenopackets can
-be used to describe other kinds of entities such as variants, examples
-on these cases will follow).
-
-We list all people inside a `persons` block:
-
-```
-persons:
- - id: #1
- date_of_birth: 1999-01-01
- sex: M
- - id: #2
- sex: M
- - id: #3
- sex: M
-```
-
-Note that in YAML, a `-` denotes an element in a list. The `person`
-block is always a list.
-
-Here we are providing a DOB for the first person, and biological sexes
-for all persons.
-
-Note the identifiers used. There are strict rules on the structure of
-identifiers used in phenopackets, and on the rules for mapping these
-to real-world entities. We will return to these in more detail
-later. In this particular case we are using hash identifiers; we use
-these when the identifiers are local to the packet and are not
-intended to be referenced from outside. If we had a global identifier
-for the person, we could use this instead.
-
-Next we will describe the conditions for these persons. In
-phenopackets, there are two distinct types of conditions: phenotypes
-and diseases.
-
-We first list any disease diagnoses. We only have one, for person
-number 1:
-
-```
-disease_diagnoses:
- - entity: #1
- disease_occurrence:
- types:
- - id: OMIM:615426
- label: amyotrophic lateral sclerosis type 20
-```
-
-Note that the diseases block is a separate block from the persons
-block. We refer back to individuals in the block using the id, rather
-than nesting the disease inside the person block. This allows for more
-flexibility in how persons and diagnoses are exchanged as messages.
-
-The value for `types` is a list. Although there will
-typically only be one disease here, there are reasons for having a
-uniform list representation, which we will return to later.
-
-We have not specified any diseases for person 2 and 3. Although we
-might assume these are not disease carriers, this is not explicitly
-stated and cannot be known for sure. We will return to how to make
-negative assertions later on.
-
-Next up is phenotype associations. Let's start with a two phenotypes,
-for person 1
-
-```
-phenotype_profile:
- - entity: #1
- phenotype:
- types:
- - id: HP:0003560
- label: Muscular dystrophy
- - entity: #1
- phenotype:
- types:
- - id: HP:0007354
- label: Amyotrophic lateral sclerosis
-
-```
-
-Although the structure may appear overly nested here, this because we
-use a highly normalized model that allows maximal hooks for
-extensibility. For example, 
-
-```
-phenotype_profile:
- - entity: #1
- phenotype:
- types:
- - id: HP:0003560
- label: Muscular dystrophy
- onset:
- types:
- - id: HP:0003584
- label: Late onset
- description: additional notes on this phenotype here
- evidence:
- - type: TAS
- source:
- id: PMID:23455423
- title: Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS
- - entity: #1
- phenotype:
- types:
- - id: HP:0007354
- label: Amyotrophic lateral sclerosis
-
-```