updated readme, improved descriptions, fixed website display error

osc-em · Oct 1, 2024 · 1fc4697 · 1fc4697
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diff --git a/README.md b/README.md
@@ -1,14 +1,28 @@
 
-# OSCEM_Schemas
-Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
-defining the electron microscopy related fields required by the OSCEM standard.
+# OSCEM schemas
+Schema for the Open Standards Community for Electron Microscopy (OSC-EM): Defining the electron microscopy-related fields required by the OSCEM standard.
 
-Core idea is a modular system that allows for the combination of several sample and method parts to describe a variety of electron microscopy use cases. All original schemas can be found as .yaml under src/oscem_schemas/schema. Files named oscem_* refer to set collections of subschemas, e.g. single particle analysis. Schemas with more precise names such as "instrument" refer to a specific subschema that can be modularily imported into oscem_* schemas. Using the linkml generator functions the overall schemas can be exported to a variety of other formats such as json-schema, jsonld, OWL and RDF. We recommend using json-schema versions for validating metadata.
+## Overview
+The OSCEM schemas are designed to standardize metadata for electron microscopy, structured modularly to accommodate various methods and use cases. Each module can represent different aspects of an experiment, such as "sample", "instrument", and "author." These modules are combined into a comprehensive schema that defines the required metadata for a specific method. This standard ensures consistency in data collection, facilitates data validation, and enhances comparability between datasets.
 
+To increase compatibility with different formats, we utilize LinkML, which allows us to export the schema to widely used formats.
+
+## currently implemented methods
+  Life sciences:
+    - cryoEM:
+      - single particle analysis
+      - Tomography:
+        - subtomogram averaging
+        - cellular tomography
+
+## Usage
+All schemas are available in YAML format under the directory src/oscem_schemas/schema. Files prefixed with oscem_* refer to collections of subschemas, such as those for single particle analysis. Schemas with more specific names, like "instrument," represent individual subschemas that can be modularly incorporated into oscem_* schemas. By using LinkML generator functions, these schemas can be exported to various formats such as JSON Schema, JSON-LD, OWL, CSV and RDF. For metadata validation, we recommend using the JSON Schema versions.
+
+## Note
 Current versions are a work in progress, details might change.
 
 ## Website
-Here you can browse all our keywords with descriptions.
+Here you can browse all our keywords for single particle analysis with descriptions:
 [https://osc-em.github.io/OSCEM_Schemas/](https://osc-em.github.io/OSCEM_Schemas/)
 
 ## Repository Structure

diff --git a/project/excel/oscem_schemas.xlsx b/project/excel/oscem_schemas.xlsx
diff --git a/project/jsonld/oscem_schemas.context.jsonld b/project/jsonld/oscem_schemas.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-09-30T11:20:21",
+      "generation_date": "2024-10-01T15:30:42",
       "source": "oscem_schemas.yaml"
    },
    "@context": {

diff --git a/project/jsonld/oscem_schemas.jsonld b/project/jsonld/oscem_schemas.jsonld
diff --git a/project/jsonschema/oscem_schemas.schema.json b/project/jsonschema/oscem_schemas.schema.json
@@ -2,7 +2,7 @@
     "$defs": {
         "Acquisition": {
             "additionalProperties": false,
-            "description": "",
+            "description": "A set of parameteres describing the data acquisition",
             "properties": {
                 "beamshift": {
                     "anyOf": [
@@ -241,7 +241,7 @@
         },
         "Any": {
             "additionalProperties": true,
-            "description": "Any type, used as the base for type-narrowing.\n\nSee https://linkml.io/linkml/schemas/advanced.html",
+            "description": "Any type, used as the base for type-narrowing.",
             "title": "Any",
             "type": [
                 "null",
@@ -252,7 +252,7 @@
             ]
         },
         "AssemblyEnum": {
-            "description": "",
+            "description": "Allowed molecular assembly values - compatible with the EMDB.",
             "enum": [
                 "FILAMENT",
                 "HELICAL ARRAY",
@@ -263,7 +263,7 @@
         },
         "Author": {
             "additionalProperties": false,
-            "description": "",
+            "description": "Details on the person performing the experiment.",
             "properties": {
                 "country": {
                     "description": "Country of the institution",
@@ -294,7 +294,7 @@
                     "type": "string"
                 },
                 "role": {
-                    "description": "Role of the author, i.e., principal investigator",
+                    "description": "Role of the author, for example principal investigator",
                     "type": [
                         "string",
                         "null"
@@ -382,7 +382,7 @@
         },
         "ChromaticAberrationCorrector": {
             "additionalProperties": false,
-            "description": "",
+            "description": "Special device used to correct instrument inherent chromatic aberration.",
             "properties": {
                 "instrument_type": {
                     "description": "Details of a given specialist instrument",
@@ -443,7 +443,7 @@
         },
         "EnergyFilter": {
             "additionalProperties": false,
-            "description": "",
+            "description": "A device used to filter for electrons with specific energy.",
             "properties": {
                 "model": {
                     "description": "Make and model of a specilized device",
@@ -499,7 +499,7 @@
                     ]
                 },
                 "funder": {
-                    "description": "funder",
+                    "description": "funding organization/person.",
                     "type": [
                         "string",
                         "null"
@@ -533,7 +533,7 @@
         },
         "Grid": {
             "additionalProperties": false,
-            "description": "A class representing a grid",
+            "description": "Details on the grid used in the experiment.",
             "properties": {
                 "film_material": {
                     "description": "Type of material the support film is made of",
@@ -699,7 +699,7 @@
         },
         "Ligand": {
             "additionalProperties": false,
-            "description": "A class representing a ligand",
+            "description": "Information on ligands if present.",
             "properties": {
                 "present": {
                     "description": "Whether the model contains any ligands",
@@ -728,7 +728,7 @@
         },
         "Molecule": {
             "additionalProperties": false,
-            "description": "A class representing a molecule",
+            "description": "More detailed information about individual molecules.",
             "properties": {
                 "expression_system": {
                     "description": "Scientific name of the organism used to produce the molecule of interest",
@@ -784,7 +784,7 @@
             "type": "object"
         },
         "MoleculeClassEnum": {
-            "description": "",
+            "description": "Allowed molecule class values - compatible with the EMDB.",
             "enum": [
                 "Antibiotic",
                 "Carbohydrate",
@@ -795,7 +795,7 @@
             "type": "string"
         },
         "OrganizationTypeEnum": {
-            "description": "",
+            "description": "Allowed values for authors organizations.",
             "enum": [
                 "Academic",
                 "Commercial",
@@ -807,7 +807,7 @@
         },
         "OverallMolecule": {
             "additionalProperties": false,
-            "description": "A class representing the overall molecule",
+            "description": "Description of the overall molecule",
             "properties": {
                 "assembly": {
                     "$ref": "#/$defs/AssemblyEnum",
@@ -848,7 +848,7 @@
         },
         "Person": {
             "additionalProperties": false,
-            "description": "",
+            "description": "personal information",
             "properties": {
                 "email": {
                     "description": "email",
@@ -892,7 +892,7 @@
         },
         "Phaseplate": {
             "additionalProperties": false,
-            "description": "",
+            "description": "Used to modulate the phase of the electron wave.",
             "properties": {
                 "instrument_type": {
                     "description": "Type of phaseplate",
@@ -962,7 +962,7 @@
         },
         "Sample": {
             "additionalProperties": false,
-            "description": "A class representing a sample",
+            "description": "Unifying class to describe the full sample.",
             "properties": {
                 "grid": {
                     "anyOf": [
@@ -1052,7 +1052,7 @@
         },
         "SpecialistOptics": {
             "additionalProperties": false,
-            "description": "",
+            "description": "Optional optics used to correct for instrument limitations.",
             "properties": {
                 "chromatic_aberration_corrector": {
                     "anyOf": [
@@ -1093,7 +1093,7 @@
         },
         "Specimen": {
             "additionalProperties": false,
-            "description": "A class representing a specimen",
+            "description": "Description of specimen handling.",
             "properties": {
                 "buffer": {
                     "description": "Name/composition of the (chemical) sample buffer during grid preparation",
@@ -1174,7 +1174,7 @@
         },
         "SphericalAberrationCorrector": {
             "additionalProperties": false,
-            "description": "",
+            "description": "Special device used to correct instrument inherent spherical aberration.",
             "properties": {
                 "instrument_type": {
                     "description": "Details of a given specialist instrument",