From 81181da398df081fe5e0e9af3b059d59ebc0fa72 Mon Sep 17 00:00:00 2001
From: saanikat <saanikatambe@gmail.com>
Date: Tue, 18 Jun 2024 15:57:06 -0400
Subject: [PATCH 1/2] encode output schema bedmess

---
 schemas/bedmess/encode_output.yaml | 60 ++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 schemas/bedmess/encode_output.yaml

diff --git a/schemas/bedmess/encode_output.yaml b/schemas/bedmess/encode_output.yaml
new file mode 100644
index 0000000..43e99be
--- /dev/null
+++ b/schemas/bedmess/encode_output.yaml
@@ -0,0 +1,60 @@
+description: Attribute Standardizer Output Schema in alignment with ENCODE schema
+
+properties:
+  File accession: 
+    type: string
+    description: "File ID/Accession"
+  File Type : 
+    type: string
+    description: "File Types (eg. bed, bigWig)"
+  File format type:
+    type: string
+    description: "File Convention/Format (eg. narrowPeak)"
+  Output type:
+    type: string
+    description: "The output type provides additional information about the expected contents in the file."
+  File assembly:
+    type: string
+    description: "Type of Genome Assemblies (eg. GRCh38)"
+  Assay:
+    type: string
+    description: "The name of the assay performed"
+  Biosample term name:
+    type: string
+    description: "The human readable ontology name used to describe the biosample."
+  Biosample type:
+    type: string
+    description: "A categorization of biosamples into major groups(eg.induced pluripotent stem cell, stem cell)."
+  Biosample Organism:
+    type: string
+    description: "The species of the biosample."
+  Biosample treatments:
+    type: string
+    description: "The name of the chemical or biological agent applied to a biosample in order to elicit a response."
+  Biosample genetic modifications methods:
+    type: string
+    description: "Experimental Techniques used for genetic modification (eg. CRISPR)"
+  Biosample genetic modifications categories:
+    type: string
+    description: "Type of genetic modification (eg. insertion)"
+  Experiment Target:
+    type: string
+    description: "Experimental Targets (eg. H3K27ac-human)"
+  Library made from:
+    type: string
+    description: "Types of libraries created from biological samples."
+  Experiment date released:
+    type: string
+    description: "Date of the experiment release"
+  Project:
+    type: string
+    description: "The project under which the experiment was performed( eg. ENCODE)"
+  Lab:
+    type: string
+    description: "Lab where the processing took place."
+  File Download URL:
+    type: string
+    description: "File Download URL"
+required:
+  - None
+

From b821d7c418b541226af27c02bf32ddc856a20228 Mon Sep 17 00:00:00 2001
From: saanikat <114712639+saanikat@users.noreply.github.com>
Date: Mon, 19 Aug 2024 22:22:04 -0400
Subject: [PATCH 2/2] fairtracks schema design for bedmess

---
 schemas/bedmess/fairtracks_output.yaml | 49 ++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 schemas/bedmess/fairtracks_output.yaml

diff --git a/schemas/bedmess/fairtracks_output.yaml b/schemas/bedmess/fairtracks_output.yaml
new file mode 100644
index 0000000..579748f
--- /dev/null
+++ b/schemas/bedmess/fairtracks_output.yaml
@@ -0,0 +1,49 @@
+description: Attribute Standardizer Output Schema in alignment with FAIRtracks schema
+
+properties:
+  global_id: 
+    type: string
+    description: "Global sample identifier, resolvable by identifiers.org"
+  local_id:
+    type: string
+    description: "Submitter-local identifier for sample (eg. S00B1LH1)"
+  species_id:
+    type: string
+    description: "Species identifier, resolvable by identifiers.org (eg. taxonomy:9606)"
+  species_name:
+    type: string
+    description: "Species name (eg. Homo sapiens)"
+  donor_age:
+    type: string
+    description: "Sample donor age ranges (eg. 50-60)"
+  donor_ethnicity:
+    type: string 
+    description: "Ethnicity of the donor (eg. Northern European)"
+  donor_health_status:
+    type: string
+    description: "Health of the donor during sample collection eg. Normal, Chronic Lymphocytic Leukemia"
+  donor_id:
+    type: string
+    description: "Donor identifier eg.182CLL"
+  donor_sex:
+    type: string
+    description: "Sex of the donor eg. Male, Female, Unknown"
+  biospecimen_class_term_id:
+    type: string
+    description: "URL of ontology term used for classification of the sample"
+  biospecimen_class_term_label:
+    type: string
+    description: "Structural unit for the classification for the sample eg. Cell, Organism Part"
+  sample_type_term_id:
+    type: string
+    description: "URL of the sample term"
+  sample_type_term_label:
+    type: string
+    description: "Main classification of the sample eg. venous blood"
+  phenotype_term_id:
+    type: string
+    description: "Identifier for the phenotype"
+  phenotype_term_label:
+    type: string
+    description: "Main phenotype related to the sample eg. Acute Myeloid Leukemia"
+