N3C-Formatted OMOP2OBO Mappings

Name: N3C-Formatted OMOP2OBO Mappings
Creator: Zenodo
Published: 2022-10-27T02:56:55+08:00

Zenodo2022-10-27 更新2026-05-25 收录

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OMOP2OBO Mappings - N3C OMOP to OBO Working group This repository stores OMOP2OBO mappings which have been processed for use within the National COVID Cohort Collaborative (N3C) Enclave. The version of the mappings stored in this repository have been specifically formatted for use within the N3C Enclave. N3C OMOP to OBO Working Group: https://covid.cd2h.org/ontology Accessing the N3C-Formatted Mappings You can access the three OMOP2OBO HPO mapping files in the Enclave from the Knowledge store using the following link: https://unite.nih.gov/workspace/compass/view/ri.compass.main.folder.1719efcf-9a87-484f-9a67-be6a29598567. The mapping set includes three files, but you only need to merge the following two files with existing data in the Enclave in order to be able to create the concept sets: OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv The first file OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv, contains columns for the OMOP concept ids and codes as well as specifies information like whether or not the OMOP concept’s descendants should be included when deriving the concept sets (defaults to FALSE). The other file OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv, contains details on the mapping’s label (i.e., the HPO curie and label in the concept_set_id field) and its provenance/evidence (the specific column to access for this information is called intention). Creating Concept Sets Merge these files together on the column named codeset_id and then join them with existing Enclave tables like concept and condition_occurrence to populate the actual concept sets. The name of the concept set can be obtained from the OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv file and is stored as a string in the column called concept_set_id. Although not ideal (but is the best way to approach this currently given what fields are available in the Enclave), to get the HPO CURIE and label will require applying a regex to this column. An example mapping is shown below (highlighting some of the most useful columns): <pre><code>codeset_id: 900000000 concept_set_id: [OMOP2OBO] hp_0002031-abnormal_esophagus_morphology concept: 23868 code: 69771008 codeSystem: SNOMED includeDescendants: False intention: Mixed - This mapping was created using the OMOP2OBO mapping algorithm (https://github.com/callahantiff/OMOP2OBO). The Mapping Category and Evidence supporting the mappings are provided below, by OMOP concept: 23868 ******* Mapping Category: Automatic Exact - Concept ------------------------------------------------ Mapping Provenance ------------------ OBO_DbXref-OMOP_ANCESTOR_SOURCE_CODE:snomed_69771008 | OBO_DbXref-OMOP_CONCEPT_SOURCE_CODE:snomed_69771008 | CONCEPT_SIMILARITY:HP_0002031_0.713</code></pre> Release Notes - v2.0.0 Preparation In order to import data into the Enclave, the following items are needed: Obtain API Token, which will be included in the authorization header (stored as GitHub Secret) Obtain username hash from the Enclave OMOP2OBO Mappings (v1.5.0) Data Concept Set Container (concept_set_container): CreateNewConceptSet Concept Set Version (code_sets): CreateNewDraftOMOPConceptSetVersion Concept Set Expression Items (concept_set_version_item): addCodeAsVersionExpression Script n3c_mapping_conversion.py Generated Output Need to have the codeset_id filled from self-generation (ideally, from a conserved range) prior to beginning any of the API steps. The current list of assigned identifiers is stored in the file named omop2obo_enclave_codeset_id_dict_v2.0.0.json. Note that in order to accommodate the 1:Many mappings the codeset ids were re-generated and rather than being ampped to HPO concepts, they are mapped to SNOMED-CT concepts. This creates a cleaner mapping and will easily scale to future mapping builds. To be consistent with OMOP tools, specifically Atlas, we have also created Atlas-formatted json files for each mapping, which are stored in the zipped directory named atlas_json_files_v2.0.0.zip. Note that as mentioned above, to enable the representation of 1:Many mappings the filenames are no longer named after HPO concepts they are now named with the OMOP concept_id and label and additional fields have been added within the JSON files that includes the HPO ids, labels, mapping category, mapping logic, and mapping evidence. File 1: concept_set_container Generated Data: OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_container.csv Columns: concept_set_id concept_set_name intention assigned_informatician assigned_sme project_id status stage n3c_reviewer alias archived created_by created_at File 2: concept_set_expression_items Generated Data: OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv Columns: codeset_id concept_id code codeSystem ontology_id ontology_label mapping_category mapping_logic mapping_evidence isExcluded includeDescendants includeMapped item_id annotation created_by created_at File 3: concept_set_version Generated Data: OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv Columns: codeset_id concept_set_id concept_set_version_title project source_application source_application_version created_at atlas_json most_recent_version comments intention limitations issues update_message status has_review reviewed_by created_by provenance atlas_json_resource_url parent_version_id is_draft Generated Output: OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_container.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv atlas_json_files_v2.0.0.zip omop2obo_enclave_codeset_id_dict_v2.0.0.json

OMOP2OBO映射集——N3C OMOP转OBO工作组 本仓库存储经适配处理后可用于国家新冠队列协作组（National COVID Cohort Collaborative，简称N3C）安全协作环境（Enclave）的OMOP2OBO映射集。本仓库所存储的映射集版本已针对N3C安全协作环境进行专属格式优化。 N3C OMOP转OBO工作组：https://covid.cd2h.org/ontology 获取N3C适配版映射集 你可通过以下链接从N3C安全协作环境的知识库中获取3个OMOP2OBO人类表型本体（Human Phenotype Ontology，简称HPO）映射文件：https://unite.nih.gov/workspace/compass/view/ri.compass.main.folder.1719efcf-9a87-484f-9a67-be6a29598567。本映射集共包含3个文件，但仅需将以下2个文件与协作区内已有数据合并，即可构建概念集（concept set）： OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv 第一个文件OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv包含OMOP概念ID、编码相关字段，并指定了推导概念集时是否需纳入对应OMOP概念的子代节点（默认值为FALSE）。第二个文件OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv则包含映射集标签（即`concept_set_id`字段中的HPO紧凑统一资源标识符（CURIE）及标签）与溯源/佐证信息（可通过名为`intention`的字段获取此类内容）。 构建概念集 以`codeset_id`列为关联键合并上述两个文件，再将合并后的数据与协作区内现有表（如`concept`表与`condition_occurrence`表）进行关联，即可生成可用的概念集。概念集名称可从OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv文件中获取，该名称以字符串形式存储在`concept_set_id`字段中。尽管此方式并非最优，但鉴于当前协作区内可用字段的限制，这仍是目前最佳实现路径——若需提取HPO CURIE与标签，需对该字段应用正则表达式（regular expression，regex）。以下展示一个映射示例（重点标注部分常用字段）： <pre><code>codeset_id: 900000000 concept_set_id: [OMOP2OBO] hp_0002031-abnormal_esophagus_morphology concept: 23868 code: 69771008 codeSystem: SNOMED includeDescendants: False intention: Mixed - This mapping was created using the OMOP2OBO mapping algorithm (https://github.com/callahantiff/OMOP2OBO). The Mapping Category and Evidence supporting the mappings are provided below, by OMOP concept: 23868 ******* Mapping Category: Automatic Exact - Concept ------------------------------------------------ Mapping Provenance ------------------ OBO_DbXref-OMOP_ANCESTOR_SOURCE_CODE:snomed_69771008 | OBO_DbXref-OMOP_CONCEPT_SOURCE_CODE:snomed_69771008 | CONCEPT_SIMILARITY:HP_0002031_0.713</code></pre> 版本发布说明——v2.0.0 准备工作 若需将数据导入N3C安全协作环境，需完成以下事项： 1. 获取API令牌（API Token），该令牌需置于请求授权头中（已作为GitHub密钥存储） 2. 从协作区获取用户名哈希值 OMOP2OBO映射集（v1.5.0） 数据文件 概念集容器（concept_set_container）：CreateNewConceptSet 概念集版本（code_sets）：CreateNewDraftOMOPConceptSetVersion 概念集表达式条目（concept_set_version_item）：addCodeAsVersionExpression 脚本文件 n3c_mapping_conversion.py 生成结果 在执行任何API操作前，需先生成`codeset_id`字段值（理想情况下使用预设的标识符范围）。当前已分配的标识符列表存储在omop2obo_enclave_codeset_id_dict_v2.0.0.json文件中。需注意：为适配一对多映射，本次重新生成了`codeset_id`，且不再将其映射至HPO概念，而是映射至SNOMED-CT概念。此举可使映射关系更清晰，且便于后续扩展至更多映射构建工作。为与OMOP工具（尤其是Atlas）保持兼容，我们还为每个映射生成了Atlas格式的JSON文件，存储在名为atlas_json_files_v2.0.0.zip的压缩目录中。需注意：如前文所述，为支持一对多映射的展示，文件名不再以HPO概念命名，而是改为使用OMOP概念ID与标签命名；同时JSON文件中新增了多个字段，涵盖HPO ID、标签、映射类别、映射逻辑与映射佐证证据。 文件1：concept_set_container 生成数据：OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_container.csv 字段列表：concept_set_id, concept_set_name, intention, assigned_informatician, assigned_sme, project_id, status, stage, n3c_reviewer, alias, archived, created_by, created_at 文件2：concept_set_expression_items 生成数据：OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv 字段列表：codeset_id, concept_id, code, codeSystem, ontology_id, ontology_label, mapping_category, mapping_logic, mapping_evidence, isExcluded, includeDescendants, includeMapped, item_id, annotation, created_by, created_at 文件3：concept_set_version 生成数据：OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv 字段列表：codeset_id, concept_set_id, concept_set_version_title, project, source_application, source_application_version, created_at, atlas_json, most_recent_version, comments, intention, limitations, issues, update_message, status, has_review, reviewed_by, created_by, provenance, atlas_json_resource_url, parent_version_id, is_draft 生成输出文件列表： OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_container.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_expression_items.csv OMOP2OBO_v2.0.0_N3C_Enclave_CSV_concept_set_version.csv atlas_json_files_v2.0.0.zip omop2obo_enclave_codeset_id_dict_v2.0.0.json

提供机构：

Zenodo

创建时间：

2022-10-27

N3C-Formatted OMOP2OBO Mappings

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