From b4bdc28fb159066bc845772aff705192042c256c Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Mon, 13 May 2024 16:39:19 -0700 Subject: [PATCH 1/4] manual curation of NMDC NCBI Attribute mappings --- assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv index d1b7755904..99a192813b 100644 --- a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv +++ b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv @@ -299,7 +299,7 @@ Biosample mineral_nutr_regm TextValue mineral_nutr_regm Biosample misc_param TextValue misc_param Biosample mod_date string Biosample n_alkanes TextValue n_alkanes -Biosample name string +Biosample name string sample_name Biosample ncbi_taxonomy_name string Biosample neon_biosample_identifiers external_identifier Biosample nitrate QuantityValue nitrate @@ -429,8 +429,8 @@ Biosample salinity_category string Biosample salinity_meth TextValue salinity_meth Biosample salt_regm TextValue salt_regm Biosample samp_capt_status samp_capt_status_enum samp_capt_status -Biosample samp_collec_device string -Biosample samp_collec_method string +Biosample samp_collec_device string samp_collect_device +Biosample samp_collec_method string sam_collect_method Biosample samp_collect_point samp_collect_point_enum samp_collect_point Biosample samp_dis_stage samp_dis_stage_enum samp_dis_stage Biosample samp_floor samp_floor_enum samp_floor From 3a5486938b3c9b68cd46c6e19ce353921a9c7dee Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Mon, 13 May 2024 16:47:29 -0700 Subject: [PATCH 2/4] fix typo in manual NCBI mapping --- assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv index 99a192813b..89d3188b07 100644 --- a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv +++ b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv @@ -430,7 +430,7 @@ Biosample salinity_meth TextValue salinity_meth Biosample salt_regm TextValue salt_regm Biosample samp_capt_status samp_capt_status_enum samp_capt_status Biosample samp_collec_device string samp_collect_device -Biosample samp_collec_method string sam_collect_method +Biosample samp_collec_method string samp_collect_method Biosample samp_collect_point samp_collect_point_enum samp_collect_point Biosample samp_dis_stage samp_dis_stage_enum samp_dis_stage Biosample samp_floor samp_floor_enum samp_floor From aa661e5116bea88c0f7ccf2c885592329a7138ae Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Mon, 13 May 2024 17:49:56 -0700 Subject: [PATCH 3/4] ignore type slot in NCBI mappings --- assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv index 89d3188b07..0b0ac9e392 100644 --- a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv +++ b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv @@ -552,7 +552,7 @@ Biosample turbidity QuantityValue turbidity Biosample tvdss_of_hcr_press QuantityValue tvdss_of_hcr_press Biosample tvdss_of_hcr_temp QuantityValue tvdss_of_hcr_temp Biosample typ_occup_density double -Biosample type string +Biosample type string MAN_IGNORE Biosample ventilation_rate QuantityValue ventilation_rate Biosample ventilation_type TextValue ventilation_type Biosample vfa QuantityValue vfa @@ -668,7 +668,7 @@ OmicsProcessing seq_quality_check TextValue OmicsProcessing start_date string OmicsProcessing target_gene TextValue OmicsProcessing target_subfragment TextValue -OmicsProcessing type string +OmicsProcessing type string MAN_IGNORE DataObject alternative_identifiers uriorcurie DataObject compression_type string DataObject data_object_type FileTypeEnum @@ -677,6 +677,6 @@ DataObject file_size_bytes bytes DataObject id uriorcurie DataObject md5_checksum string DataObject name string -DataObject type string +DataObject type string MAN_IGNORE DataObject url string DataObject was_generated_by Activity From e205a84848c7abd6324b67944f386f875d50a8af Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Mon, 13 May 2024 18:00:15 -0700 Subject: [PATCH 4/4] ignore general name field PlannedProcess classes --- assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv index 0b0ac9e392..a9cb419011 100644 --- a/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv +++ b/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv @@ -609,7 +609,7 @@ Extraction has_output NamedThing Extraction id uriorcurie Extraction input_mass QuantityValue Extraction instrument_name string -Extraction name string +Extraction name string MAN_IGNORE Extraction processing_institution processing_institution_enum Extraction protocol_link Protocol Extraction qc_comment string @@ -627,7 +627,7 @@ LibraryPreparation id uriorcurie LibraryPreparation instrument_name string LibraryPreparation library_preparation_kit string LibraryPreparation library_type LibraryTypeEnum -LibraryPreparation name string +LibraryPreparation name string MAN_IGNORE LibraryPreparation pcr_cycles integer LibraryPreparation processing_institution processing_institution_enum LibraryPreparation protocol_link Protocol @@ -649,7 +649,7 @@ OmicsProcessing insdc_bioproject_identifiers external_identifier OmicsProcessing insdc_experiment_identifiers external_identifier OmicsProcessing instrument_name string OmicsProcessing mod_date string -OmicsProcessing name string +OmicsProcessing name string MAN_IGNORE OmicsProcessing ncbi_project_name string OmicsProcessing nucl_acid_amp TextValue OmicsProcessing nucl_acid_ext TextValue @@ -676,7 +676,7 @@ DataObject description string description DataObject file_size_bytes bytes DataObject id uriorcurie DataObject md5_checksum string -DataObject name string +DataObject name string MAN_IGNORE DataObject type string MAN_IGNORE DataObject url string DataObject was_generated_by Activity