Schema

The schema structure is designed to be simple and intuitive. Here is a basic skeleton of the expected schema structure:

%YAML 1.2
---
# metadata: general information about the schema
metadata:
  id: ""          # unique identifier for the schema
  name: ""        # name of the schema
  description: "" # description of the schema
  version: ""     # version of the schema
  curators: []    # A list of curators of the schema

# engine: specifies the computational tools and additional parameters used for sequence
#         analysis.
engine:
  type: ""            # The type of tool used to generate the data
  tool: ""            # The tool used to generate the data
  params: {}          # Additional parameters for the tool
    min_pident: int   # Minimum percent identity for the tool
    min_coverage: int # Minimum percent coverage for the tool

# targets: Lists the specific sequence targets such as genes, proteins, or markers that the
#          schema will analyze. These should be included in the associated sequence query data
targets: []

# aliases: groups multiple targets under a common name for easier reference
aliases:
  - name: ""     # name of the alias
    targets: []  # list of targets that are part of the alias

# types: define specific combinations of targets and aliases to form distinct types
types:
  - name: ""     # name of the profile
    targets: []  # list of targets (can use aliases) that are part of the profile
    excludes: [] # list of targets (or aliases) that will automatically fail the type

From this schema we have a few sections:

metadata: general information about the schema
engine: computational requirements for sequence analysis
targets: lists the sequence targets such as genes, proteins, or markers
aliases: groups multiple targets under a common name for easier reference
profiles: defines combinations of targets and aliases to form typing profiles

Within each section there are additional fields that will be descibed in the next sections.

metadata¶

The metadata section provides general information about the schema. This includes:

Field	Type	Description
id	string	A unique identifier for the schema
name	string	The name of the schema
description	string	A brief description of the schema
version	string	The version of the schema
curators	list	A list of curators of the schema

engine¶

The engine section specifies the computational tools used for sequence analysis.

Field	Type	Description
type	string	The type of engine used for analysis
tool	string	The specific tool to be used for the engine
params	dict	Additional parameters for the tool to use as default

targets¶

The targets section lists the specific sequence targets such as genes, proteins, or markers that the schema will analyze. These should be included in the associated sequence query data.

Field	Type	Description
targets	list	A list of targets to be analyzed

aliases¶

aliases are a convenient way to group multiple targets under a common name for easier reference.

Field	Type	Description
name	string	The name of the alias
targets	list	A list of targets that are part of the alias

types¶

The types section defines specific combinations of targets and aliases to form distinct types.

Field	Type	Description
name	string	The name of the profile
targets	list	A list of targets (or aliases) that are part of the type
excludes	list	A list of targets (or aliases) that will automatically fail the type

Example Schema: Partial SCCmec Typing¶

Here is an example of a partial schema for SCCmec typing:

%YAML 1.2
---
# metadata: general information about the schema
metadata:
  id: "sccmec_partial"                                # unique identifier for the schema
  name: "SCCmec Typing"                              # name of the schema
  description: "A partial schema for SCCmec typing"  # description of the schema
  version: "0.0.1"                                     # version of the schema
  curators:                                          # A list of curators of the schema
    - "Robert Petit"

# engine: specifies the computational tools and additional parameters used for sequence
#         analysis.
engine:
  type: blast   # The type of tool used to generate the data
  tool: blastn  # The tool used to generate the data
  params:       # Additional parameters for the tool
    min_pident: 80   # Minimum percent identity for the tool
    min_coverage: 80 # Minimum percent coverage for the tool

# targets: Lists the specific sequence targets such as genes, proteins, or markers that the
#          schema will analyze. These should be included in the associated sequence query data
targets:
  - "ccrA1"
  - "ccrA2"
  - "ccrA3"
  - "ccrB1"
  - "ccrB2"
  - "ccrB3"
  - "IS431"
  - "IS1272"
  - "mecA"
  - "mecI"
  - "mecR1"

# aliases: groups multiple targets under a common name for easier reference
aliases:
  - name: "ccr Type 1"           # name of the alias
    targets: ["ccrA1", "ccrB1"]  # list of targets that are part of the alias
  - name: "ccr Type 2"
    targets: ["ccrA2", "ccrB2"]
  - name: "ccr Type 3"
    targets: ["ccrA3", "ccrB3"]
  - name: "mec Class A"
    targets: ["IS431", "mecA", "mecR1", "mecI"]
  - name: "mec Class B"
    targets: ["IS431", "mecA", "mecR1", "IS1272"]

# types: define specific combinations of targets and aliases to form distinct types
types:
  - name: "I"          # name of the profile
    targets:           # list of targets (can use aliases) that are part of the profile
      - "ccr Type 1"
      - "mec Class B"
  - name: "II"
    targets:
      - "ccr Type 2"
      - "mec Class A"
  - name: "III"
    targets:
      - "ccr Type 3"
      - "mec Class A"
  - name: "IV"
    targets:
      - "ccr Type 2"
      - "mec Class B"

From this schema, camlhmp can generate a typing tool that can be used to analyze input assemblies. This is only a partial schema, as there are many more SCCmec types and subtypes. But using this schema it should be straight forward to add additional targets and profiles.