{"action":"created","comment":{"url":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/pulls/comments/215894846","pull_request_review_id":153261388,"id":215894846,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxNTg5NDg0Ng==","diff_hunk":"@@ -0,0 +1,537 @@\n+# The Human Cell Atlas: Metadata Schema Style and Formatting Guide\n+\n+## Table of Contents\n+- [Introduction](#introduction)\n+- [Schema model](#schema-model)\n+- [Schema style and formatting](#schema-style-and-formatting)\n+- [Field style and formatting](#field-style-and-formatting)\n+- [General rules](#general-rules)\n+\n+## Introduction\n+\n+>**DISCLAIMER:** At this time, the HCA Metadata Standard development team is actively working towards adhering to this style and formatting guide. In some cases, the standard might not yet follow all the guidelines outlined in this document. Your patience is appreciated!\n+\n+This document describes the style and formatting rules followed by the HCA Metadata Standard for JSON schemas and fields. The goals of the Metadata Standard are to improve the accessibility, (re-)usability, and quality of data submitted to the HCA. In order to develop a high-quality, robust Metadata Standard, we propose the following guidelines and aim to adhere to them as the standard evolves and adapts to changing technologies. \n+\n+**What is in this document**\n+- General style guidelines for naming and formatting for metadata schemas and fields\n+- Rationale for why the guidelines were chosen\n+\n+**Who should be reading this document?**\n+- HCA DCP developers\n+- Anyone reporting a bug in the schema\n+- Members of external projects seeking alignment with HCA metadata standards\n+\n+**What *isn't* in this document?**\n+- Directions for [requesting or suggesting changes](contributing.md) to the metadata schema\n+\n+## Schema model\n+\n+The JSON format that is the canonical representation of the HCA Metadata Standard is a programming language-neutral, persistent method of storing data structures. See [ECMA-404 The JSON Data Interchange Standard](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf) specification for technical details of the format. JSON objects are analogous to C structs, objects in JAVA and Python, and to an extent, SQL tables. The design of JSON metadata objects follows the common approaches used in designing computational data structures for programmers. The schema is used to describe the contents of the JSON data objects for both programmatic access and human understanding.\n+\n+The JSON schemas that make up the HCA Metadata Standard are publicly developed and maintained in GitHub [HumanCellAtlas/metadata-schema](https://github.com/HumanCellAtlas/metadata-schema). The official published and released JSON schemas are hosted at [schema.humancellatlas.org](https://schema.humancellatlas.org/).\n+\n+As implemented for the HCA Metadata Standard, each JSON schema contains a set of related fields (also called properties). For example, the `cell_line.json` schema contains fields specific to describing cell lines. The following sections describe style and formatting rules followed by HCA metadata schemas and fields.\n+\n+## Schema style and formatting\n+\n+The following attributes are required for each metadata schema in the HCA metadata standard. \n+\n+1. **$schema:** The JSON draft version being used.\n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            ...\n+        }\n+\n+1. **description:** A clear, concise description of the schema. \n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            ...\n+        }\n+\n+1. **additionalProperties:** Whether additional fields not in the schema will be allowed. The *additionalProperties* attribute should always be set to `false`. Currently, user-supplied fields are not accepted without consultation. The metadata team actively encourages data contributors who want new fields to contact them so the new fields can be added to the schema following the process for requesting updates to the Metadata Standard to include new fields is outlined in our contributing documentation [here](contributing.md#requesting-or-suggesting-changes-to-the-metadata-schema).\n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            \"additionalProperties\": false,\n+            ...\n+        }\n+\n+1. **required:** An array indicating which fields in the schema are required. If no fields are required, omit this attribute. Fields are determined to be required if they are necessary to enable downstream analysis and visualization.\n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            \"additionalProperties\": false,\n+            \"required\": [\n+                \"describedBy\",\n+                \"schema_type\",\n+                \"biomaterial_core\",\n+                \"model_for_organ\"\n+            ],\n+            ...\n+        }\n+\n+1. **title:** A title for the schema. The *title* is the user-friendly name of the schema which should be in sentence case. This attribute is displayed in the metadata spreadsheet and the Data Browser.\n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            \"additionalProperties\": false,\n+            \"required\": [\n+                \"describedBy\",\n+                \"schema_type\",\n+                \"biomaterial_core\",\n+                \"model_for_organ\"\n+            ],\n+            \"title\": \"Organoid\",\n+            ...\n+        }\n+\n+1. **name:** A programmatic name for the schema. The *name* is the name of the schema which should be in all lowercase and snake_case. This attribute is used by the DCP software to identify the schema, and the *name* should match the filename of the schema absent the `.json` file extension.\n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            \"additionalProperties\": false,\n+            \"required\": [\n+                \"describedBy\",\n+                \"schema_type\",\n+                \"biomaterial_core\",\n+                \"model_for_organ\"\n+            ],\n+            \"title\": \"Organoid\",\n+            \"name\": \"organoid\",\n+            ...\n+        }\n+\n+1. **type** and **properties:** The *type* of the schema (should always be `object`) followed by the metadata fields (`properties`).  \n+\n+    Example:\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            \"additionalProperties\": false,\n+            \"required\": [\n+                \"describedBy\",\n+                \"schema_type\",\n+                \"biomaterial_core\",\n+                \"model_for_organ\"\n+            ],\n+            \"title\": \"Organoid\",\n+            \"name\": \"organoid\",\n+            \"type\": \"object\",\n+            \"properties\": {\n+                ...\n+            }\n+        }\n+\n+1. **$id:** A persistent URI for the schema. The `$id` attribute is **not** included in JSON schemas in GitHub. Instead, it is inserted automatically at the time schemas are published to the HCA Metadata Standard at [schema.humancellatlas.org](https://schema.humancellatlas.org/).\n+\n+    Example:\n+    \n+    *GitHub*\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            ...\n+        }\n+    \n+    *schema.humancellatlas.org*\n+    \n+        {\n+            \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n+            \"$id\": \"http://schema.humancellatlas.org/type/biomaterial/8.3.4/organoid\",\n+            \"description\": \"Information about an organoid biomaterial.\",\n+            ...\n+        }\n+        \n+    The `$id` attribute is a resolvable URL which points to the published schema hosted by the Human Cell Atlas. This attribute is inserted at build time as it must contain the version of the schema which is not defined within the schema document itself on GitHub. The list of latest schema versions is maintained in the `versions.json` file in GitHub, separate from the JSON schema documents themselves, in order to enable unit testing. The specification for using the JSON `$id` keyword can be found [here](http://json-schema.org/latest/json-schema-core.html#rfc.section.8.2)\n+\n+## Field style and formatting\n+\n+Naming fields in data structures is challenging because of the desire to optimize both clarity to avoid ambiguity and brevity to avoid cumbersome code. To help chose field names that are both clear and brief, it is vital to consider the context in which field names are referred. In structured programming languages, an *unqualified* field name is a name local to its context (in this case, to its schema). When combined with its context (in this case, with its schema name), an unqualified field name becomes a *qualified* field name, which is usually expressed as a concatenation of the context name and the unqualified field name. For example:\n+    \n+> HCA unqualified field name: `diseases`\n+>\n+> HCA qualified field name: `donor_organism.diseases`\\\n+> HCA qualified field name: `specimen_from_organism.diseases`\n+\n+In the HCA, qualified field names are used by the Ingestion Service to convert metadata spreadsheets to JSON, by the Data Store Service (DSS) to index JSON documents, and by the Secondary Analysis Service and Data Browser to query for metadata in the DSS. Unqualified field names are not used in isolation, although corresponding *user-friendly* names (see below) are used in the metadata spreadsheet, the Data Browser, and the Metadata Dictionary on the Data Portal. \n+\n+Some principles the HCA Metadata Standard follows regarding field and schema names are:\n+\n+1. *Field and schema names are programming constructs, not GUI constructs.* Field and schema names are only intended for use by programmers, including those writing textual queries. Attempting to have a field name that is both a good GUI name and a good programmatic name makes the naming problem more difficult. For example, field name changes to make a GUI clearer potentially creates breaking changes for code accessing the data structures. Additionally, GUI implementation from field and schemas names is difficult as different labels for data are often needed depending on how data are being presented. Therefore, field and schemas names should be used as keys to look up natural language terms (*e.g.* to look up schema titles and user-friendly field names).\n+\n+1. *Unqualified field names need to be unique within a schema, but do not need to be globally unique among all schemas.* Within a single JSON schema, no two field names should be identical. However, the same field name can exist in two different schemas, as their qualified names will be different. For example, the field name `diseases` can exist in both the `donor_organism.json` and `specimen_from_organism.json` schemas because the qualified field names are `donor_organism.diseases` and `specimen_from_organism.diseases`, respectively.\n+\n+1. *Qualified field names need to be unique among all schemas.* Fully qualified field names need to be globally unique across the HCA Metadata Standard. Qualified field names are used by multiple services, thus they need to be globally unique so that only a single field is accessed/returned for a given qualified field name request.\n+\n+1. *Unqualified field names should not contain context.* Unqualified field names do not stand alone, meaning they are not accessed or used outside of their context (*i.e.* their schema). Therefore, additional context should be removed from unqualified field names unless there is justification for including it<sup>**</sup>. For example:","path":"docs/schema_style_guide.md","position":188,"original_position":188,"commit_id":"a3d9bcb89352241b1c7f5940ceea1a546382900e","original_commit_id":"a3d9bcb89352241b1c7f5940ceea1a546382900e","user":{"login":"malloryfreeberg","id":10993501,"node_id":"MDQ6VXNlcjEwOTkzNTAx","avatar_url":"https://avatars2.githubusercontent.com/u/10993501?v=4","gravatar_id":"","url":"https://api.github.com/users/malloryfreeberg","html_url":"https://github.com/malloryfreeberg","followers_url":"https://api.github.com/users/malloryfreeberg/followers","following_url":"https://api.github.com/users/malloryfreeberg/following{/other_user}","gists_url":"https://api.github.com/users/malloryfreeberg/gists{/gist_id}","starred_url":"https://api.github.com/users/malloryfreeberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malloryfreeberg/subscriptions","organizations_url":"https://api.github.com/users/malloryfreeberg/orgs","repos_url":"https://api.github.com/users/malloryfreeberg/repos","events_url":"https://api.github.com/users/malloryfreeberg/events{/privacy}","received_events_url":"https://api.github.com/users/malloryfreeberg/received_events","type":"User","site_admin":false},"body":"The `<sup>**</sup>` bit is meant to make the two asterisks superscripts. There is no nice markdown way to do this, so html-style tags are used. The superscript asterisks are meant to correspond to the \"**Potential caveats\" note below the example, but if that doesn't make sense then I can just remove the double asterisks.","created_at":"2018-09-07T09:10:28Z","updated_at":"2018-09-07T09:10:28Z","html_url":"https://github.com/HumanCellAtlas/metadata-schema/pull/534#discussion_r215894846","pull_request_url":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/pulls/534","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/pulls/comments/215894846"},"html":{"href":"https://github.com/HumanCellAtlas/metadata-schema/pull/534#discussion_r215894846"},"pull_request":{"href":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/pulls/534"}},"in_reply_to_id":215683771},"pull_request":{"url":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/pulls/534","id":213562852,"node_id":"MDExOlB1bGxSZXF1ZXN0MjEzNTYyODUy","html_url":"https://github.com/HumanCellAtlas/metadata-schema/pull/534","diff_url":"https://github.com/HumanCellAtlas/metadata-schema/pull/534.diff","patch_url":"https://github.com/HumanCellAtlas/metadata-schema/pull/534.patch","issue_url":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/issues/534","number":534,"state":"open","locked":false,"title":"Metadata Style Guide","user":{"login":"malloryfreeberg","id":10993501,"node_id":"MDQ6VXNlcjEwOTkzNTAx","avatar_url":"https://avatars2.githubusercontent.com/u/10993501?v=4","gravatar_id":"","url":"https://api.github.com/users/malloryfreeberg","html_url":"https://github.com/malloryfreeberg","followers_url":"https://api.github.com/users/malloryfreeberg/followers","following_url":"https://api.github.com/users/malloryfreeberg/following{/other_user}","gists_url":"https://api.github.com/users/malloryfreeberg/gists{/gist_id}","starred_url":"https://api.github.com/users/malloryfreeberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malloryfreeberg/subscriptions","organizations_url":"https://api.github.com/users/malloryfreeberg/orgs","repos_url":"https://api.github.com/users/malloryfreeberg/repos","events_url":"https://api.github.com/users/malloryfreeberg/events{/privacy}","received_events_url":"https://api.github.com/users/malloryfreeberg/received_events","type":"User","site_admin":false},"body":"<!-- Please provide a meaningful title for your PR. Do not keep the default title. -->\r\n<!-- Use the following GitHub keyword if your PR completely resolves an issue: \"Fixes #123\" -->\r\n\r\n<!-- Describe how you tested this PR, and how you will test the feature after it is merged. -->\r\n\r\n<!-- If this PR updates the metadata schema, add a note describing the feature which will be added to the changelog. \r\nIndicate whether the update is to something Added, Changed, Removed, Fixed, Deprecated, or Securit. \r\nUncomment the heading below:\r\n### Release notes -->\r\n\r\nThis PR adds a Metadata Style Guide to the metadata-schema repo.","created_at":"2018-09-06T10:05:29Z","updated_at":"2018-09-07T09:10:28Z","closed_at":null,"merged_at":null,"merge_commit_sha":"50887ce3e5b4c591805348fc40d5101c39825f0d","assignee":null,"assignees":[],"requested_reviewers":[{"login":"daniwelter","id":1267974,"node_id":"MDQ6VXNlcjEyNjc5NzQ=","avatar_url":"https://avatars2.githubusercontent.com/u/1267974?v=4","gravatar_id":"","url":"https://api.github.com/users/daniwelter","html_url":"https://github.com/daniwelter","followers_url":"https://api.github.com/users/daniwelter/followers","following_url":"https://api.github.com/users/daniwelter/following{/other_user}","gists_url":"https://api.github.com/users/daniwelter/gists{/gist_id}","starred_url":"https://api.github.com/users/daniwelter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daniwelter/subscriptions","organizations_url":"https://api.github.com/users/daniwelter/orgs","repos_url":"https://api.github.com/users/daniwelter/repos","events_url":"https://api.github.com/users/daniwelter/events{/privacy}","received_events_url":"https://api.github.com/users/daniwelter/received_events","type":"User","site_admin":false},{"login":"willrockout","id":19597324,"node_id":"MDQ6VXNlcjE5NTk3MzI0","avatar_url":"https://avatars2.githubusercontent.com/u/19597324?v=4","gravatar_id":"","url":"https://api.github.com/users/willrockout","html_url":"https://github.com/willrockout","followers_url":"https://api.github.com/users/willrockout/followers","following_url":"https://api.github.com/users/willrockout/following{/other_user}","gists_url":"https://api.github.com/users/willrockout/gists{/gist_id}","starred_url":"https://api.github.com/users/willrockout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/willrockout/subscriptions","organizations_url":"https://api.github.com/users/willrockout/orgs","repos_url":"https://api.github.com/users/willrockout/repos","events_url":"https://api.github.com/users/willrockout/events{/privacy}","received_events_url":"https://api.github.com/users/willrockout/received_events","type":"User","site_admin":false},{"login":"cjvillar","id":20974239,"node_id":"MDQ6VXNlcjIwOTc0MjM5","avatar_url":"https://avatars0.githubusercontent.com/u/20974239?v=4","gravatar_id":"","url":"https://api.github.com/users/cjvillar","html_url":"https://github.com/cjvillar","followers_url":"https://api.github.com/users/cjvillar/followers","following_url":"https://api.github.com/users/cjvillar/following{/other_user}","gists_url":"https://api.github.com/users/cjvillar/gists{/gist_id}","starred_url":"https://api.github.com/users/cjvillar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjvillar/subscriptions","organizations_url":"https://api.github.com/users/cjvillar/orgs","repos_url":"https://api.github.com/users/cjvillar/repos","events_url":"https://api.github.com/users/cjvillar/events{/privacy}","received_events_url":"https://api.github.com/users/cjvillar/received_events","type":"User","site_admin":false},{"login":"hewgreen","id":23357242,"node_id":"MDQ6VXNlcjIzMzU3MjQy","avatar_url":"https://avatars0.githubusercontent.com/u/23357242?v=4","gravatar_id":"","url":"https://api.github.com/users/hewgreen","html_url":"https://github.com/hewgreen","followers_url":"https://api.github.com/users/hewgreen/followers","following_url":"https://api.github.com/users/hewgreen/following{/other_user}","gists_url":"https://api.github.com/users/hewgreen/gists{/gist_id}","starred_url":"https://api.github.com/users/hewgreen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hewgreen/subscriptions","organizations_url":"https://api.github.com/users/hewgreen/orgs","repos_url":"https://api.github.com/users/hewgreen/repos","events_url":"https://api.github.com/users/hewgreen/events{/privacy}","received_events_url":"https://api.github.com/users/hewgreen/received_events","type":"User","site_admin":false},{"login":"zperova","id":38244059,"node_id":"MDQ6VXNlcjM4MjQ0MDU5","avatar_url":"https://avatars0.githubusercontent.com/u/38244059?v=4","gravatar_id":"","url":"https://api.github.com/users/zperova","html_url":"https://github.com/zperova","followers_url":"https://api.github.com/users/zperova/followers","following_url":"https://api.github.com/users/zperova/following{/other_user}","gists_url":"https://api.github.com/users/zperova/gists{/gist_id}","starred_url":"https://api.github.com/users/zperova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zperova/subscriptions","organizations_url":"https://api.github.com/users/zperova/orgs","repos_url":"https://api.github.com/users/zperova/repos","events_url":"https://api.github.com/users/zperova/events{/privacy}","received_events_url":"https://api.github.com/users/zperova/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[{"id":944449609,"node_id":"MDU6TGFiZWw5NDQ0NDk2MDk=","url":"https://api.github.com/repos/HumanCellAtlas/metadata-schema/labels/documentation","name"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