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Welcome to the OMH To FHIR Quick-Start Guide

Quick Start Mapping Guide For Mapping OMH Schema Mappings to FHIR Elements

Measurements such as steps or heart rate are modeled using OMH schemas. These models can be used to represent instance of the measurement "over the wire" in JSON. The OMH schema can be transformed into FHIR

The following 9 OMH schemas used to represent instance of the measurement "over the wire" in JSON:

  1. blood glucose
  2. blood pressure [add property cuff position]
  3. body temperature
  4. body weight
  5. heart rate [resting]
  6. O2 saturation
  7. respiratory rate
  8. sleep duration [--> total sleep time ]
  9. step count [change datatype of property step_count to unit_value]

are composed of the of the OMH header element a body which contains the datapoint schema represents the body's properties. They are transformed into FHIR using a series of mapping steps to convert the sctructure and content into a corresponding FHIR Observation Profile.

OMH Header Element to FHIR Element Mapping Table

Each OMH schema for a datapoint is composed of the 'header' and 'body, This table summarizes the mapping of the OMH header elements to the corresponding OMH to FHIR Observation Profile element. Each datapoint schema represents the body's properties and will be covered individually.

OMH element FHIR element
template profile OMH to FHIR Observation Profile
header.id Observation.identifier
header.creation_date_time Observation.issued
header.schema_id None
header.schema_id.namespace None
header.schema_id.name Observation.category,Observation.code ( see datapoint mapping table below )
header.schema_id.version None
header.acquisition_provenance None
header.acquisition_provenance.source_name Observation.device
header.acquisition_provenance.source_data_point_id Observation.identifier
header.acquisition_provenance.source_creation_date_time None
header.acquisition_provenance.modication_data_time None
header.acquisition_provenance.modality Observation.device.extension
header.user_id Observation.subject
{: .grid}

The detailed mapping for the OMH header can be found here...

OMH DataPoint Element to FHIR Element Mapping Table

Each Datapoint is represented by the body properties and this table summarizes of the OMH datapoint schema type as represented by the header.schema_id.name element to the corresponding FHIR Observation category and 'code' elements and default units for quantitative measures.

header.schema_id.name Observation.category.code Observation.code.system Observation.code.code Observation.code.display observation_value_quantity_unit(s) (list)
blood_glucose laboratory http://loinc.org 2339-0 Glucose Mass/volume in Blood ['mg/dL', 'mmol/L']
blood_pressure* vital-signs http://loinc.org 85354-9 Blood pressure panel with all children optional None
body_temperature vital-signs http://loinc.org 8310-5 Body temperature ['K','F','C']
body_weight vital-signs http://loinc.org 29463-7 Body weight ['kg', 'g', 'lb']
heart_rate vital-signs http://loinc.org 8867-4 Heart rate ['beats/min']
oxygen_saturation vital-signs http://loinc.org 59408-5 Oxygen saturation in Arterial blood by Pulse oximetry ['%']
respiratory_rate vital-signs http://loinc.org 9279-1 Respiratory Rate ['breaths/min']
sleep_duration physical-activity http://snomed.info/id 248263006 Duration of sleep (observable entity) ['sec', 'min', 'h']
step_count physical-activity http://loinc.org 55423-8 Number of steps in unspecified time Pedometer ['steps']

Data Point Component Mapping Table

Blood Pressure Datapoints has these additional properties that are represented by the FHIR Observation.component element in FHIR. This table summarizes these OMH datapoint schema properties and list the corresponding OMH propertied name in the Component Name column and its corresponding FHIR Observation component code and valuetype attributes. This table is used along with the OMH to FHIR concept mapping table to to populate the the FHIR Observation profile.

Component Name Component Code System Component Code Code Component Code Display Component Value Type
cuff_position http://loinc.org NNNN-N Position of cuff [add property cuff position]
diastolic_blood_pressure http://loinc.org 8462-4 Diastolic blood pressure valueQuantity
systolic_blood_pressure http://loinc.org 8480-6 Systolic blood pressure valueQuantity

OMH Header to FHIR Observation Detailed Mapping

The following Table provides the detailed mapping for the OMH Header to the OMH to FHIR Observation Profile TODO: add link to profile:

Index OMH Header Element FHIR Attribute Derived Mapping Comments
1 header-1.2.json OMH to FHIR Observation Profile
2.1 header.id identifier[0].value
2.2 header.id identifier[0].system https://omh.org/shimmer/ids fixed to 'https://omh.org/shimmer/ids'
3 header.creation_date_time issued 1:1 mapping of header.creation_date_time
4 header.schema_id None
5 header.schema_id.namespace None
6A.1 header.schema_id.name category[0].coding[0].code data_point_mapping_table "Maps to column 'Observation.category.code'
6A.2 header.schema_id.name category[0].coding[0].system http://hl7.org/fhir/observation-category "fixed to ""http://hl7.org/fhir/observation-category""
6B.1 header.schema_id.name code.coding[0].code data_point_mapping_table['Observation.code.code'] "Maps to column 'Observation.code.code'
6B.2 code.coding[0].system data_point_mapping_table['Observation.code.system'] "Maps to column 'Observation.code.system'
6B.3 code.coding[0].display data_point_mapping_table['Observation.code.display'] "Maps to column 'Observation.code.display'
7 header.schema_id.version None
8 header.acquisition_provenance None
9 header.acquisition_provenance.source_name device.display 1:1 mapping of header.acquisition_provenance.source_name
10.1 header.acquisition_provenance.source_data_point_id identifier[1].value 1:1 mapping of header.acquisition_provenance.source_data_point_id
10.2 identifier[1].system https://omh.org/source/ids fixed to 'https://omh.org/source/ids'
11 header.acquisition_provenance.source_creation_date_time None
12 header.acquisition_provenance.modication_date_time None
13.1 header.acquisition_provenance.modality device.extension[0].valueCode 1:1 mapping of header.acquisition_provenance.modality
13.2 device.extension[0].url http://www.fhir.org/mfhir/StructureDefinition/extenion-modality fixed to 'http://www.fhir.org/mfhir/StructureDefinition/extenion-modality'
14.1 header.user_id subject.identifier.value 1:1 mapping of string
14.2 subject.identifier.system https://omh.org/shimmerM/patient_id fixed to 'https://omh.org/shimmer/patient_id'

Example Mapping:

The following OMH Header schema instance:

"header": {
  "id": "243c773b-8936-407e-9c23-270d0ea49cc4",
  "creation_date_time": "2015-09-10T12:43:39.138-06:00",
  "acquisition_provenance": {
    "source_name": "Jawbone UP API",
    "modality": "sensed",
    "source_updated_date_time": "2015-09-10T18:43:39Z"
  },
  "schema_id": {
    "namespace": "omh",
    "name": "blood_glucose",
    "version": "1.0"
  },
  "user_id": "306a1202-410d-11e8-842f-0ed5f89f718b"
}

Maps to the FHIR Observation resource:

{
   "issued": "2015-09-10T12:43:39.138-06:00",
   "resourceType": "Observation",
   "category": [
      {
         "coding": [
            {
               "code": "laboratory",
               "display": "Laboratory",
               "system": "http://hl7.org/fhir/observation-category"
            }
         ]
      }
   ],
   "code": {
      "coding": [
         {
            "code": "2339-0",
            "display": "Glucose Mass/volume in Blood",
            "system": "http://loinc.org"
         }
      ]
   },
   "device": {
      "display": "Jawbone UP API",
      "extension": [
         {
            "valueCode": "sensed",
            "url": "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_observation_device_modality"
         }
      ]
   },
   "identifier": [
      {
         "value": "243c773b-8936-407e-9c23-270d0ea49cc4",
         "system": "https://omh.org/shimmer/ids"
      }
   ],
   "meta": {
      "profile": [
         "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_profile_quantitative_observation"
      ]
   },
   "status": "unknown",
   "subject": {
      "identifier": {
         "value": "306a1202-410d-11e8-842f-0ed5f89f718b",
         "system": "https://omh.org/shimmer/patient_ids"
      }
   }
}

OMH HeartRate DataPoint to FHIR Observation Detailed Mapping

The following Table provides the detailed mapping for the OMH HeartRate DataPoint to the OMH to FHIR Observation Profile TODO: add link to profile:

Index OMH Header Element FHIR Attribute Derived Mapping Comments
1 heart-rate-1.1.json OMH to FHIR Observation Profile
2.1 body.heart_rate Observation.valueQuantity see valueQuantity elements below
2.2 body.heart_rate.value Observation.valueQuantity.value 1:1 mapping of number
2.3 body.heart_rate.unit Observation.valueQuantity.unit 1:1 mapping of string
2.4 valueQuantity.system http://unitsofmeasure.org fixed to 'http://unitsofmeasure.org'
2.5 valueQuantity.code OMH_FHIR_Concept_Maps['body.heart_rate.unit'] Concept Mapping
3 body.effective_time_frame Observation.effective[x] Mappping depends on type- see below
5 body.effective_time_frame.date_time Observation.effectiveDateTime 1:1 mapping of body.effective_time_frame.date_time
4 body.effective_time_frame.time_interval Observation.effectivePeriod see effectivePeriod.elements below
6 body.effective_time_frame.time_interval.start_date_time Observation.effectivePeriod.start 1:1 mapping of body.effective_time_frame.time_interval.start_date_time
7 body.effective_time_frame.time_interval.end_date_time Observation.effectivePeriod.end 1:1 mapping of body.effective_time_frame.time_interval.end_date_time
8 body.user_notes Observation.comment 1:1 mapping of body.user_notes
9 body.descriptive_statistic Observation.coding[1] Map descriptive statistic to the OMH to FHIR additional Observation codings ( code system http://www.fhir.org/guides/mfhir/omh_fhir_observation_codes).
10 body.temporal_relationship_to_physical_activity Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list
11 body.temporal_relationship_to_sleep Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list

Example Mapping:

The following OMH HeartRate schema instance:

{
  "body": {
 "effective_time_frame": {
    "date_time": "2013-02-05T07:25:00Z"
 },
 "blood_glucose": {
    "value": 95,
    "unit": "mg/dL"
 }
}
}

Maps to this FHIR Observation fragment

...
"effectiveDateTime": "2013-02-05T07:25:00Z",
"valueQuantity": {
   "value": 95,
   "code": "mg/dL",
   "unit": "mg/dL",
   "system": "http://unitsofmeasure.org"
...

to make this this FHIR Observation when combine with the OMH Header

{
   "issued": "2015-09-10T12:43:39.138-06:00",
   "effectiveDateTime": "2013-02-05T07:25:00Z",
   "resourceType": "Observation",
   "valueQuantity": {
      "value": 95,
      "code": "mg/dL",
      "unit": "mg/dL",
      "system": "http://unitsofmeasure.org"
   },
   "category": [
      {
         "coding": [
            {
               "code": "laboratory",
               "display": "Laboratory",
               "system": "http://hl7.org/fhir/observation-category"
            }
         ]
      }
   ],
   "code": {
      "coding": [
         {
            "code": "2339-0",
            "display": "Glucose Mass/volume in Blood",
            "system": "http://loinc.org"
         }
      ]
   },
   "device": {
      "display": "Jawbone UP API",
      "extension": [
         {
            "valueCode": "sensed",
            "url": "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_observation_device_modality"
         }
      ]
   },
   "identifier": [
      {
         "value": "243c773b-8936-407e-9c23-270d0ea49cc4",
         "system": "https://omh.org/shimmer/ids"
      }
   ],
   "meta": {
      "profile": [
         "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_profile_quantitative_observation"
      ]
   },
   "status": "unknown",
   "subject": {
      "identifier": {
         "value": "306a1202-410d-11e8-842f-0ed5f89f718b",
         "system": "https://omh.org/shimmer/patient_ids"
      }
   }
}

OMH Body Temperature DataPoint to FHIR Observation Detailed Mapping

The following Table provides the detailed mapping for the OMH Body Temperature DataPoint to the OMH to FHIR Observation Profile TODO: add link to profile:

Index OMH Body Temperature Element FHIR Attribute Derived Mapping Comments
1 body-temperature-2.0.json OMH to FHIR Observation Profile
2.1 body_temperature Observation.valueQuantity see valueQuantity elements below
2.2 body_temperature.value Observation.valueQuantity.value 1:1 mapping of number
2.3 body_temperature.unit Observation.valueQuantity.unit 1:1 mapping of string
2.4 valueQuantity.system http://unitsofmeasure.org fixed to 'http://unitsofmeasure.org'
2.5 valueQuantity.code OMH_FHIR_Concept_Maps['body.body_temperature.unit']Concept Mapping
3 body.effective_time_frame Observation.effective[x] Mappping depends on type- see below
5 body.effective_time_frame.date_time Observation.effectiveDateTime 1:1 mapping of body.effective_time_frame.date_time
4 body.effective_time_frame.time_interval Observation.effectivePeriod see effectivePeriod.elements below
8.1 body.effective_time_frame.time_interval.start_date_time Observation.effectivePeriod.start 1:1 mapping of body.effective_time_frame.time_interval.start_date_time
8.0 body.effective_time_frame.time_interval.end_date_time Observation.effectivePeriod.end 1:1 mapping of body.effective_time_frame.time_interval.end_date_time
8.1 measurement_location Observation.bodySite See bodySite elements below
8.2 Observation.bodySIte.coding[0].system OMH_FHIR_Concept_Maps['body.X'][0]for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code System'
8.3 Observation.bodySIte.coding[0].code OMH_FHIR_Concept_Maps['body.X'][1]for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code'
8.4 Observation.bodySIte.coding[0].display OMH_FHIR_Concept_Maps['body.X'][2]for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code Display'
9 body.descriptive_statistic Observation.coding[1] Map descriptive statistic to the OMH to FHIR additional Observation codings ( code system http://www.fhir.org/guides/mfhir/omh_fhir_observation_codes).
10 body.temporal_relationship_to_physical_activity Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list
11 body.temporal_relationship_to_sleep Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list

Example Mapping:

The following OMH Body Temperature schema instance:

{
  "body": {
   "effective_time_frame": {
      "time_interval": {
         "end_date_time": "2015-02-06T06:00:00Z",
         "start_date_time": "2015-02-05T06:00:00Z"
      }
   },
   "descriptive_statistic": "maximum",
   "body_temperature": {
      "value": 96.5,
      "unit": "F"
   },
   "measurement_location": "oral"
  }
}

Maps to this FHIR Observation fragment

...
"code": {
   "coding": [
      {
         "code": "body-temperature-maximum",
         "display": "Body Temperature Maximum",
         "system": "http://hl7.org/fhir/omh_fhir_observation_codes"
      }
   ]
},
{
   "effectivePeriod": {
      "end": "2015-02-06T06:00:00Z",
      "start": "2015-02-05T06:00:00Z"
   },
   "valueQuantity": {
      "value": 96.5,
      "code": "[degF]",
      "unit": "F",
      "system": "http://unitsofmeasure.org"
   },
   "bodySite": {
      "coding": [
         {
            "code": "oral",
            "system": "http://www.fhir.org/guides/mfhir/CodeSystem/intervention-administration-route"
         }
      ],
      "text": "oral"
   },
...

to make this this FHIR Observation when combine with the OMH Header

{
   "meta": {
      "profile": [
         "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_profile_quantitative_observation"
      ]
   },
   "bodySite": {
      "coding": [
         {
            "code": "oral",
            "system": "http://www.fhir.org/guides/mfhir/CodeSystem/intervention-administration-route"
         }
      ],
      "text": "oral"
   },
   "category": [
      {
         "coding": [
            {
               "code": "vital-signs",
               "display": "Vital Signs",
               "system": "http://hl7.org/fhir/observation-category"
            }
         ]
      }
   ],
   "code": {
      "coding": [
         {
            "code": "8310-5",
            "display": "Body temperature",
            "system": "http://loinc.org"
         },
         {
            "code": "body-temperature-maximum",
            "display": "Body Temperature-Maximum",
            "system": "http://hl7.org/fhir/omh_fhir_observation_codes"
         }
      ]
   },
   "device": {
      "extension": [
         {
            "url": "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_observation_device_modality",
            "valueCode": "sensed"
         }
      ],
      "display": "Jawbone UP API"
   },
   "effectivePeriod": {
      "end": "2015-02-06T06:00:00Z",
      "start": "2015-02-05T06:00:00Z"
   },
   "identifier": [
      {
         "system": "https://omh.org/shimmer/ids",
         "value": "243c773b-8936-407e-9c23-270d0ea49cc4"
      }
   ],
   "issued": "2015-09-10T12:43:39.138-06:00",
   "status": "unknown",
   "subject": {
      "identifier": {
         "system": "https://omh.org/shimmer/patient_ids",
         "value": "306a1202-410d-11e8-842f-0ed5f89f718b"
      }
   },
   "valueQuantity": {
      "code": "[degF]",
      "system": "http://unitsofmeasure.org",
      "unit": "F",
      "value": 96.5
   },
   "resourceType": "Observation"
}

OMH Blood Glucose DataPoint to FHIR Observation Detailed Mapping

The following Table provides the detailed mapping for the OMH Blood Glucose DataPoint to the OMH to FHIR Observation Profile TODO: add link to profile:

Index OMH Blood Glucose Element FHIR Attribute Derived Mapping Comments
1 blood-glucose-2.0.json OMH to FHIR Observation Profile
2.1 body.blood_glucose Observation.valueQuantity see valueQuantity elements below
2.2 body.blood_glucose.value Observation.valueQuantity.value 1:1 mapping of number
2.3 body.blood_glucose.unit Observation.valueQuantity.unit 1:1 mapping of string
2.4 valueQuantity.system http://unitsofmeasure.org fixed to 'http://unitsofmeasure.org'
2.5 valueQuantity.code OMH_FHIR_Concept_Maps['body.heart_rate.unit'] Concept Mapping
3 body.effective_time_frame Observation.effective[x] Mappping depends on type- see below
5 body.effective_time_frame.date_time Observation.effectiveDateTime 1:1 mapping of body.effective_time_frame.date_time
4 body.effective_time_frame.time_interval Observation.effectivePeriod see effectivePeriod.elements below
6 body.effective_time_frame.time_interval.start_date_time Observation.effectivePeriod.start 1:1 mapping of body.effective_time_frame.time_interval.start_date_time
7 body.effective_time_frame.time_interval.end_date_time Observation.effectivePeriod.end 1:1 mapping of body.effective_time_frame.time_interval.end_date_time
8 body.user_notes Observation.note[0].text 1:1 mapping of body.user_notes, optionally can add author and time to the FHIR Annotation datatype
9.1 body.specimen_source Observation.extension extension url = 'http://www.fhir.org/mfhir/StructureDefinition/extension-specimenCode'
9.2 Observation.extension[0].url ttp://www.fhir.org/mfhir/StructureDefinition/extension-specimenCode fixed to 'ttp://www.fhir.org/mfhir/StructureDefinition/extension-specimenCode'
9.3 Observation.extension[0].valueCodeableConcept
9.4 Observation.extension[0].valueCodeableConcept.coding[0].system OMH_FHIR_Concept_Maps['body.X'][0] for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code System'
9.5 Observation.extension[0].valueCodeableConcept.coding[0].code OMH_FHIR_Concept_Maps['body.X'][1] for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code'
9.6 Observation.extension[0].valueCodeableConcept.coding[0].display OMH_FHIR_Concept_Maps['body.X'][2] for row = body.X = OMH to FHIR Concept Mapping Table maps to column 'Concept Code Display'
10 body.descriptive_statistic Observation.coding[1] Map descriptive statistic to the OMH to FHIR additional Observation codings ( code system http://www.fhir.org/guides/mfhir/omh_fhir_observation_codes).
11 body.temporal_relationship_to_physical_activity Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list
12 body.temporal_relationship_to_sleep Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list
13 temporal_relationship_to_meal Observation.component component_mapping_table A mapping table between OMH schema ('datapoint_variables') and FHIR Observation Component data elements. Multiple components mapping are appended as a list

Example Mapping:

The following OMH Blood Glucose schema instance:

{
  "body": {
   "descriptive_statistic": "minimum",
   "effective_time_frame": {
      "time_interval": {
         "end_date_time": "2013-06-05T07:25:00Z",
         "start_date_time": "2013-02-05T07:25:00Z"
      }
   },
   "blood_glucose": {
      "value": 120,
      "unit": "mg/dL"
   }
}

Maps to this FHIR Observation fragment

...
"code": {
   "coding": [
      {
         "code": "blood-glucose-minimum",
         "display": "Blood Glucose Minimum",
         "system": "http://hl7.org/fhir/omh_fhir_observation_codes"
      }
   ]
},
{
   "effectivePeriod": {
      "end": "2013-06-05T07:25:00Z",
      "start": "2013-02-05T07:25:00Z"
   },
   "valueQuantity": {
      "value": 120,
      "code": "mg/dL",
      "unit": "mg/dL",
      "system": "http://unitsofmeasure.org"
   }
...

to make this this FHIR Observation when combine with the OMH Header

{
   "effectivePeriod": {
      "end": "2013-06-05T07:25:00Z",
      "start": "2013-02-05T07:25:00Z"
   },
   "issued": "2015-09-10T12:43:39.138-06:00",
   "resourceType": "Observation",
   "valueQuantity": {
      "value": 120,
      "code": "mg/dL",
      "unit": "mg/dL",
      "system": "http://unitsofmeasure.org"
   },
   "category": [
      {
         "coding": [
            {
               "code": "laboratory",
               "display": "Laboratory",
               "system": "http://hl7.org/fhir/observation-category"
            }
         ]
      }
   ],
   "code": {
      "coding": [
         {
            "code": "2339-0",
            "display": "Glucose Mass/volume in Blood",
            "system": "http://loinc.org"
         },
         {
            "code": "blood-glucose-minimum",
            "display": "Blood Glucose Minimum",
            "system": "http://hl7.org/fhir/omh_fhir_observation_codes"
         }
      ]
   },
   "device": {
      "display": "Jawbone UP API",
      "extension": [
         {
            "valueCode": "sensed",
            "url": "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_observation_device_modality"
         }
      ]
   },
   "identifier": [
      {
         "value": "243c773b-8936-407e-9c23-270d0ea49cc4",
         "system": "https://omh.org/shimmer/ids"
      }
   ],
   "meta": {
      "profile": [
         "http://www.fhir.org/mfhir/StructureDefinition/omh_fhir_profile_quantitative_observation"
      ]
   },
   "status": "unknown",
   "subject": {
      "identifier": {
         "value": "306a1202-410d-11e8-842f-0ed5f89f718b",
         "system": "https://omh.org/shimmer/patient_ids"
      }
   }
}

PUNCHLIST

  • Mapping and example for

    1. blood glucose - done
    2. blood pressure [add property cuff position]
    3. body temperature - done
    4. body weight
    5. heart rate [resting] - done
    6. O2 saturation
    7. respiratory rate
    8. sleep duration [-- total sleep time ]
    9. step count [change datatype of property step_count to unit_value]

  • add linke to the concept mapping

  • add links:

    1. spreadsheets
    2. terminology
    3. concept Mapping
    4. FHIR profiles
    5. sample code

  • validate examples to FHIR R4

  • source documentation is all in markdown - consider other documentation toolilng like makedocs or Jekyll for better formatting