diff --git a/docs/background.html b/docs/background.html
index 01b32efc..a1d9190c 100644
--- a/docs/background.html
+++ b/docs/background.html
@@ -531,7 +531,7 @@ Background
The community is actively using the OMOP Common Data Model for their
various research purposes. Those tools will continue to be maintained
and supported, and information about this work is available in the public domain.
+href="https://www.github.com/ohdsi">public domain.
The OMOP Common Data Model will continue to be an open-source
community standard for observational healthcare data. The model
specifications and associated work products will be placed in the public
diff --git a/docs/cdm53.html b/docs/cdm53.html
index b2d288c4..300c7a76 100644
--- a/docs/cdm53.html
+++ b/docs/cdm53.html
@@ -618,7 +618,7 @@
person
gender identity it should be stored in the OBSERVATION
table. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
gender concepts. Please refer to the THEMIS
repository for detailed conventions on how to populate this field.
@@ -772,7 +772,7 @@ person
of human races and ethnic backgrounds, this is not a perfect system.
Mixed races are not supported. If a clear race or ethnic background
cannot be established, use Concept_Id 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Race Concepts.
@@ -808,7 +808,7 @@ person
Only use this field if you have US-based data and a source of this
information. Do not attempt to infer Ethnicity from the race or ethnic
background of the Person. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
ethnicity concepts
|
@@ -8990,7 +8990,7 @@ provider
specialties, or, 2. Choose the specialty that occurs most often for the
provider. Concepts in this field should be Standard with a domain of
Provider. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -9077,7 +9077,7 @@ provider
|
If given, put a concept from the gender domain representing the recorded
gender of the provider. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -9521,7 +9521,7 @@ payer_plan_period
|
Map the Plan directly to a standard CONCEPT_ID in the ‘Plan’ vocabulary
(Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts). This vocabulary is not exhaustive so if there is a value
missing, please see the custom
@@ -9729,7 +9729,7 @@ payer_plan_period
|
Map the stop reason directly to a standard CONCEPT_ID with a domain of
‘Plan Stop Reason’ (Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts). If one does not exist visit the Custom
Concepts pate for more information.
diff --git a/docs/cdm54.html b/docs/cdm54.html
index 5008a881..6aeaee5d 100644
--- a/docs/cdm54.html
+++ b/docs/cdm54.html
@@ -586,7 +586,7 @@ Current Support for CDM v5.4
| ATLAS |
ATLAS is an open source software tool for researchers to conduct
scientific analyses on standardized observational data. Demo |
+href="https://atlas-demo.ohdsi.org/">Demo
✔️ |
❗ |
@@ -726,7 +726,7 @@ person
gender identity it should be stored in the OBSERVATION
table. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
gender concepts. Please refer to the THEMIS
repository for detailed conventions on how to populate this field.
@@ -880,7 +880,7 @@ person
of human races and ethnic backgrounds, this is not a perfect system.
Mixed races are not supported. If a clear race or ethnic background
cannot be established, use Concept_Id 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Race Concepts.
@@ -916,7 +916,7 @@ person
Only use this field if you have US-based data and a source of this
information. Do not attempt to infer Ethnicity from the race or ethnic
background of the Person. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
ethnicity concepts
|
@@ -9668,7 +9668,7 @@ provider
specialties, or, 2. Choose the specialty that occurs most often for the
provider. Concepts in this field should be Standard with a domain of
Provider. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -9755,7 +9755,7 @@ provider
|
If given, put a concept from the gender domain representing the recorded
gender of the provider. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -10199,7 +10199,7 @@ payer_plan_period
|
Map the Plan directly to a standard CONCEPT_ID in the ‘Plan’ vocabulary
(Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts). This vocabulary is not exhaustive so if there is a value
missing, please see the custom
@@ -10407,7 +10407,7 @@ payer_plan_period
|
Map the stop reason directly to a standard CONCEPT_ID with a domain of
‘Plan Stop Reason’ (Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts). If one does not exist visit the Custom
Concepts pate for more information.
diff --git a/docs/cdm54Changes.html b/docs/cdm54Changes.html
index 564267b7..e8e5af89 100644
--- a/docs/cdm54Changes.html
+++ b/docs/cdm54Changes.html
@@ -506,7 +506,7 @@ Changes by Table
from CDM v5.3 -> CDM v5.4
For a full description of each table and field listed here, please
-see the CDM
+see the CDM
specification.
Notation:
diff --git a/docs/cdm54erd.html b/docs/cdm54erd.html
index c8466b61..87537535 100644
--- a/docs/cdm54erd.html
+++ b/docs/cdm54erd.html
@@ -449,7 +449,7 @@ OMOP CDM v5.4 ERD
entity-relationship diagram and we crowned two winners! Martijn Schuemie
and Renske Los created the best printable version and Vishnu
Chandrabalan created the best interactive version.
+href="https://omop-erd.surge.sh/">interactive version.
|
@@ -861,7 +861,7 @@ person
of human races and ethnic backgrounds, this is not a perfect system.
Mixed races are not supported. If a clear race or ethnic background
cannot be established, use Concept_Id 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Race Concepts.
|
@@ -897,7 +897,7 @@ person
Only use this field if you have US-based data and a source of this
information. Do not attempt to infer Ethnicity from the race or ethnic
background of the Person. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
ethnicity concepts
|
@@ -9897,7 +9897,7 @@ provider
specialties, or, 2. Choose the specialty that occurs most often for the
provider. Concepts in this field should be Standard with a domain of
Provider. If not available, set to 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -9984,7 +9984,7 @@ provider
|
If given, put a concept from the gender domain representing the recorded
gender of the provider. If not available, set to 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -10370,7 +10370,7 @@ payer_plan_period
vocabulary available for this information. The point is to stratify on
this information and identify if Persons have the same payer, though the
name of the Payer is not necessary. If not available, set to 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Payer&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -10460,7 +10460,7 @@ payer_plan_period
this information and identify if Persons have the same health benefit
Plan though the name of the Plan is not necessary. If not available, set
to 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -10647,7 +10647,7 @@ payer_plan_period
vocabulary available for this information. The point is to stratify on
this information and identify if Persons have the same sponsor though
the name of the sponsor is not necessary. If not available, set to 0. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Sponsor&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
@@ -10762,7 +10762,7 @@ payer_plan_period
Map the stop reason directly to a standard CONCEPT_ID. If one does not
exists please contact the vocabulary team. There is no global controlled
vocabulary available for this information. Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
Concepts.
|
diff --git a/docs/dataModelConventions.html b/docs/dataModelConventions.html
index 4898da41..f04babb2 100644
--- a/docs/dataModelConventions.html
+++ b/docs/dataModelConventions.html
@@ -565,7 +565,7 @@ Fields
standard_concept attribute for the corresponding term is true), which
serves as the primary basis for all standardized analytics. For example,
CONDITION_CONCEPT_ID = 31967
+href="https://athena.ohdsi.org/search-terms/terms/31967">31967
contains the reference value for the SNOMED concept of ‘Nausea’ |
@@ -573,7 +573,7 @@ Fields
Foreign key into the Standardized Vocabularies representing the
concept and terminology used in the source data, when applicable. For
example, CONDITION_SOURCE_CONCEPT_ID = 45431665
+href="https://athena.ohdsi.org/search-terms/terms/45431665">45431665
denotes the concept of ‘Nausea’ in the Read terminology; the analogous
CONDITION_CONCEPT_ID might be 31967, since SNOMED-CT is the Standardized
Vocabulary for most clinical diagnoses and findings. |
diff --git a/docs/faq.html b/docs/faq.html
index 53313ca1..401b0702 100644
--- a/docs/faq.html
+++ b/docs/faq.html
@@ -529,7 +529,7 @@ OMOP CDM Frequently Asked Questions
full builder freely available on github that has been
written for a variety of data sources.
-The community forums are also
+
The community forums are also
a great place to ask questions if you are stuck or need guidance on how
to represent your data in the common data model. Members are usually
very responsive!
@@ -677,13 +677,13 @@ Vocabulary Mapping
If your data use any of the 55 source vocabularies that are currently
supported, the mappings have been done for you. The full list is
available from the open-source ATHENA tool under
+href="https://athena.ohdsi.org/search-terms/terms">ATHENA tool under
the download tab (see below). You can choose to download the ten vocabulary
tables from there as well – you will need a copy in your environment
if you plan on building a CDM.
-The ATHENA
+
The ATHENA
tool also allows you to explore the vocabulary before downloading it if
you are curious about the mappings or if you have a specific code in
mind and would like to know which standard concept it is associated
@@ -694,7 +694,7 @@
Vocabulary Mapping
Yes, all mappings are available in the Concept_relationship
table (which can be downloaded from ATHENA). Each
+href="https://athena.ohdsi.org/search-terms/terms">ATHENA). Each
value in a supported source terminology is assigned a Concept_id (which
is considered non-standard). Each Source_concept_id will have a mapping
to a Standard_concept_id. For example:
@@ -804,13 +804,13 @@ OHDSI Tools
While there are a variety of tools freely available from the
community, these are the most widely used:
-- ACHILLES – a
+
- ACHILLES – a
stand-alone tool for database characterization
-- ATLAS - an
+
- ATLAS - an
integrated platform for vocabulary exploration, cohort definition, case
review, clinical characterization, incidence estimation,
population-level effect estimation design, and patient-level prediction
-design (link to
+design (link to
github)
- ARACHNE – a tool to
facilitate distributed network analyses
diff --git a/docs/index.html b/docs/index.html
index edd432ee..b940dd64 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -468,7 +468,7 @@ The CDM Working Group
as a living model by soliciting and responding to requests from the
community based on use cases and research purposes. For more information
on the CDM refresh process please see the description here.
+href="https://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">here.
You will find information on our meetings and links to join at the end
of this page.
@@ -509,7 +509,7 @@
Calendar
Current CDM Version
The current CDM version is CDM v5.4,
+href="https://ohdsi.github.io/CommonDataModel/cdm54.html">CDM v5.4,
depicted below. This CDM version was developed over the course of a year
by considering requests that were sent via our issues page.
@@ -517,12 +517,12 @@
Current CDM Version
multiple ways: through discussions at the weekly OHDSI Community calls,
discussions with the OHDSI Steering Committee, and discussions with all
potentially affected workgroups. The
final
+href="https://ohdsi.github.io/CommonDataModel/cdm54Changes.html">final
changes were then delivered to the Community through a new R package
designed to dynamically generate the DDLs and documentation for all
supported SQL dialects. Looking for an entity-relationshop diagram?
Click
here!
+href="https://ohdsi.github.io/CommonDataModel/cdm54erd.html">here!
@@ -653,7 +653,7 @@ CDM WG Important Links
CDM
Github
Process
+href="https://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">Process
for adopting CDM and Vocabulary changes
diff --git a/rmd/background.Rmd b/rmd/background.Rmd
index 0c6486dd..5296a4ca 100644
--- a/rmd/background.Rmd
+++ b/rmd/background.Rmd
@@ -17,7 +17,7 @@ The results of OMOP's research has been widely published and presented at scient
The OMOP Legacy continues...
-The community is actively using the OMOP Common Data Model for their various research purposes. Those tools will continue to be maintained and supported, and information about this work is available in the [public domain](http://www.github.com/ohdsi).
+The community is actively using the OMOP Common Data Model for their various research purposes. Those tools will continue to be maintained and supported, and information about this work is available in the [public domain](https://www.github.com/ohdsi).
The OMOP Common Data Model will continue to be an open-source community standard for observational healthcare data. The model specifications and associated work products will be placed in the public domain, and the entire research community is encouraged to use these tools to support everybody's own research activities.
diff --git a/rmd/cdm54.Rmd b/rmd/cdm54.Rmd
index f6f02ebe..bbb8b278 100644
--- a/rmd/cdm54.Rmd
+++ b/rmd/cdm54.Rmd
@@ -34,7 +34,7 @@ The table below details which OHDSI tools support CDM v5.4. There are two levels
|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emoji::emoji("heavy_check_mark")`| `r emoji::emoji("exclamation")`
|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations against an OMOP CDM instance. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
-|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
+|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](https://atlas-demo.ohdsi.org/) |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")`
|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")`*
|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
diff --git a/rmd/cdm54erd.Rmd b/rmd/cdm54erd.Rmd
index aab1e3e1..65bf5e4e 100644
--- a/rmd/cdm54erd.Rmd
+++ b/rmd/cdm54erd.Rmd
@@ -23,6 +23,6 @@ script src = "https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"
});
```
-Late in 2022 we held a community contest to find the best entity-relationship diagram and we crowned two winners! Martijn Schuemie and Renske Los created the best printable version and Vishnu Chandrabalan created the best [interactive version](http://omop-erd.surge.sh/).
+Late in 2022 we held a community contest to find the best entity-relationship diagram and we crowned two winners! Martijn Schuemie and Renske Los created the best printable version and Vishnu Chandrabalan created the best [interactive version](https://omop-erd.surge.sh/).
](images/erd.jpg){width=150%}
diff --git a/rmd/dataModelConventions.Rmd b/rmd/dataModelConventions.Rmd
index 59d686ba..6fe2dd35 100644
--- a/rmd/dataModelConventions.Rmd
+++ b/rmd/dataModelConventions.Rmd
@@ -24,8 +24,8 @@ Notation|Description
---------------------|--------------------------------------------------
|_SOURCE_VALUE|Verbatim information from the source data, typically used in ETL to map to CONCEPT_ID, and not to be used by any standard analytics. For example, CONDITION_SOURCE_VALUE = '787.02' was the ICD-9 code captured as a diagnosis from the administrative claim.|
|_ID|Unique identifiers for key entities, which can serve as foreign keys to establish relationships across entities. For example, PERSON_ID uniquely identifies each individual. VISIT_OCCURRENCE_ID uniquely identifies a PERSON encounter at a point of care.|
-|_CONCEPT_ID|Foreign key into the Standardized Vocabularies (i.e. the standard_concept attribute for the corresponding term is true), which serves as the primary basis for all standardized analytics. For example, CONDITION_CONCEPT_ID = [31967](http://athena.ohdsi.org/search-terms/terms/31967) contains the reference value for the SNOMED concept of 'Nausea'|
-|_SOURCE_CONCEPT_ID|Foreign key into the Standardized Vocabularies representing the concept and terminology used in the source data, when applicable. For example, CONDITION_SOURCE_CONCEPT_ID = [45431665](http://athena.ohdsi.org/search-terms/terms/45431665) denotes the concept of 'Nausea' in the Read terminology; the analogous CONDITION_CONCEPT_ID might be 31967, since SNOMED-CT is the Standardized Vocabulary for most clinical diagnoses and findings.|
+|_CONCEPT_ID|Foreign key into the Standardized Vocabularies (i.e. the standard_concept attribute for the corresponding term is true), which serves as the primary basis for all standardized analytics. For example, CONDITION_CONCEPT_ID = [31967](https://athena.ohdsi.org/search-terms/terms/31967) contains the reference value for the SNOMED concept of 'Nausea'|
+|_SOURCE_CONCEPT_ID|Foreign key into the Standardized Vocabularies representing the concept and terminology used in the source data, when applicable. For example, CONDITION_SOURCE_CONCEPT_ID = [45431665](https://athena.ohdsi.org/search-terms/terms/45431665) denotes the concept of 'Nausea' in the Read terminology; the analogous CONDITION_CONCEPT_ID might be 31967, since SNOMED-CT is the Standardized Vocabulary for most clinical diagnoses and findings.|
|_TYPE_CONCEPT_ID|Delineates the origin of the source information, standardized within the Standardized Vocabularies. For example, DRUG_TYPE_CONCEPT_ID can allow analysts to discriminate between 'Pharmacy dispensing' and 'Prescription written'|
## **Vocabulary**
diff --git a/rmd/faq.Rmd b/rmd/faq.Rmd
index 68d30434..2ffc3e79 100644
--- a/rmd/faq.Rmd
+++ b/rmd/faq.Rmd
@@ -15,7 +15,7 @@ During the extract, transform, load (ETL) process of converting a data source in
You or someone in your organization will need to create a process to build your CDM. Don’t worry though, you are not alone! The open nature of the community means that much of the code that other participants have written to transform their own data is available for you to use. If you have a data license for a large administrative claims database like IBM MarketScan® or Optum’s Clinformatics® Extended Data Mart, chances are that someone has already done the legwork. Here is one example of a full builder freely available on [github](https://github.com/OHDSI/ETL-CDMBuilder) that has been written for a variety of data sources.
-The [community forums](http://forums.ohdsi.org/) are also a great place to ask questions if you are stuck or need guidance on how to represent your data in the common data model. Members are usually very responsive!
+The [community forums](https://forums.ohdsi.org/) are also a great place to ask questions if you are stuck or need guidance on how to represent your data in the common data model. Members are usually very responsive!
**3. Are any tables or fields optional?**
@@ -67,15 +67,15 @@ An observation period is considered as the time at which a patient is at-risk to
**12. Do I have to map my source codes to Standard Concepts myself? Are there vocabulary mappings that already exist for me to leverage?**
-If your data use any of the 55 source vocabularies that are currently supported, the mappings have been done for you. The full list is available from the open-source [ATHENA](http://athena.ohdsi.org/search-terms/terms) tool under the download tab (see below). You can choose to download the ten [vocabulary tables](https://ohdsi.github.io/CommonDataModel/cdm54.html#Standardized-Vocabularies) from there as well – you will need a copy in your environment if you plan on building a CDM.
+If your data use any of the 55 source vocabularies that are currently supported, the mappings have been done for you. The full list is available from the open-source [ATHENA](https://athena.ohdsi.org/search-terms/terms) tool under the download tab (see below). You can choose to download the ten [vocabulary tables](https://ohdsi.github.io/CommonDataModel/cdm54.html#Standardized-Vocabularies) from there as well – you will need a copy in your environment if you plan on building a CDM.
-The [ATHENA](http://athena.ohdsi.org/search-terms/terms) tool also allows you to explore the vocabulary before downloading it if you are curious about the mappings or if you have a specific code in mind and would like to know which standard concept it is associated with; just click on the search tab and type in a keyword to begin searching.
+The [ATHENA](https://athena.ohdsi.org/search-terms/terms) tool also allows you to explore the vocabulary before downloading it if you are curious about the mappings or if you have a specific code in mind and would like to know which standard concept it is associated with; just click on the search tab and type in a keyword to begin searching.
**13. If I want to apply the mappings myself, can I do so? Are they transparent to all users?**
-Yes, all mappings are available in the [Concept_relationship](https://ohdsi.github.io/CommonDataModel/cdm54.html#CONCEPT_RELATIONSHIP) table (which can be downloaded from [ATHENA](http://athena.ohdsi.org/search-terms/terms)). Each value in a supported source terminology is assigned a Concept_id (which is considered non-standard). Each Source_concept_id will have a mapping to a Standard_concept_id. For example:
+Yes, all mappings are available in the [Concept_relationship](https://ohdsi.github.io/CommonDataModel/cdm54.html#CONCEPT_RELATIONSHIP) table (which can be downloaded from [ATHENA](https://athena.ohdsi.org/search-terms/terms)). Each value in a supported source terminology is assigned a Concept_id (which is considered non-standard). Each Source_concept_id will have a mapping to a Standard_concept_id. For example:
@@ -129,8 +129,8 @@ Changes are first listed in the release notes on the [github](https://github.com
While there are a variety of tools freely available from the community, these are the most widely used:
-* [ACHILLES](http://www.github.com/ohdsi/achilles) – a stand-alone tool for database characterization
-* [ATLAS](http://www.ohdsi.org/web/atlas/#/home) - an integrated platform for vocabulary exploration, cohort definition, case review, clinical characterization, incidence estimation, population-level effect estimation design, and patient-level prediction design ([link to github](http://www.github.com/ohdsi/atlas))
+* [ACHILLES](https://www.github.com/ohdsi/achilles) – a stand-alone tool for database characterization
+* [ATLAS](https://www.ohdsi.org/web/atlas/#/home) - an integrated platform for vocabulary exploration, cohort definition, case review, clinical characterization, incidence estimation, population-level effect estimation design, and patient-level prediction design ([link to github](https://www.github.com/ohdsi/atlas))
* [ARACHNE](https://github.com/OHDSI/ArachneUI) – a tool to facilitate distributed network analyses
* [WhiteRabbit](https://github.com/OHDSI/whiterabbit) - an application that can be used to analyse the structure and contents of a database as preparation for designing an ETL
* [RabbitInAHat](https://github.com/OHDSI/whiterabbit) - an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit
diff --git a/rmd/index.Rmd b/rmd/index.Rmd
index 7319956a..8d35833f 100644
--- a/rmd/index.Rmd
+++ b/rmd/index.Rmd
@@ -17,7 +17,7 @@ If not otherwise specified, all OHDSI content is subject to the [Creative Common
## The CDM Working Group
-The CDM is managed by the OHDSI CDM Working Group. If you would like to join our group please fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model" to be added to our Microsoft Teams environment. This working group endeavors to maintain the OMOP CDM as a living model by soliciting and responding to requests from the community based on use cases and research purposes. For more information on the CDM refresh process please see the description [here](http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html). You will find information on our meetings and links to join at the end of this page.
+The CDM is managed by the OHDSI CDM Working Group. If you would like to join our group please fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model" to be added to our Microsoft Teams environment. This working group endeavors to maintain the OMOP CDM as a living model by soliciting and responding to requests from the community based on use cases and research purposes. For more information on the CDM refresh process please see the description [here](https://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html). You will find information on our meetings and links to join at the end of this page.
### Calendar
@@ -44,7 +44,7 @@ calendar(calendarData, navigation = TRUE, defaultDate = Sys.Date()) %>%
## Current CDM Version
-The current CDM version is [CDM v5.4](http://ohdsi.github.io/CommonDataModel/cdm54.html), depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our [issues page](https://github.com/OHDSI/CommonDataModel/issues). The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The [final changes](http://ohdsi.github.io/CommonDataModel/cdm54Changes.html) were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects. Looking for an entity-relationshop diagram? Click [here](http://ohdsi.github.io/CommonDataModel/cdm54erd.html)!
+The current CDM version is [CDM v5.4](https://ohdsi.github.io/CommonDataModel/cdm54.html), depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our [issues page](https://github.com/OHDSI/CommonDataModel/issues). The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The [final changes](https://ohdsi.github.io/CommonDataModel/cdm54Changes.html) were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects. Looking for an entity-relationshop diagram? Click [here](https://ohdsi.github.io/CommonDataModel/cdm54erd.html)!
- [Link to DDLs for CDM v5.4](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4)
- [Link to ReadMe for instructions on how to use the R package](https://github.com/OHDSI/CommonDataModel/tree/master#readme)
@@ -64,7 +64,7 @@ The table below details which OHDSI tools support CDM v5.4. There are two levels
|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emoji::emoji("heavy_check_mark")`| `r emoji::emoji("exclamation")`
|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations against an OMOP CDM instance. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
-|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
+|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](https://atlas-demo.ohdsi.org/) |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")`
|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("heavy_check_mark")`*
|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emoji::emoji("heavy_check_mark")`|`r emoji::emoji("exclamation")`
@@ -78,4 +78,4 @@ The table below details which OHDSI tools support CDM v5.4. There are two levels
- [Google Drive Location](https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu)
- [Running Agenda](https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing)
- [CDM Github](https://github.com/OHDSI/CommonDataModel)
-- [Process for adopting CDM and Vocabulary changes](http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html)
+- [Process for adopting CDM and Vocabulary changes](https://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html)
diff --git a/docs/cdm60.html b/docs/cdm60.html
index ecedc8df..85fdddfd 100644
--- a/docs/cdm60.html
+++ b/docs/cdm60.html
@@ -514,9 +514,9 @@