From 7d9bec92cc36dfe5c310e3d9ad2036490647d7d6 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 15 Oct 2020 12:02:38 +0200
Subject: [PATCH] chore, update readme and doc
---
docs/advanced/datasets.md | 247 +-------------------------------------
docs/releases/v2.3.0.md | 6 +-
2 files changed, 9 insertions(+), 244 deletions(-)
diff --git a/docs/advanced/datasets.md b/docs/advanced/datasets.md
index ac2602edd..c9d837b79 100644
--- a/docs/advanced/datasets.md
+++ b/docs/advanced/datasets.md
@@ -2,248 +2,9 @@
Human Brain Project Knowledge Graph is a metadata database consisting of datasets contributed by collaborators of the Human Brain Project and curated by human curoators in order to ensure the highest standards.
-The interactive atlas viewer fetches the datasets relevant to the template space and parcellation atlas selected by the user using the following conditions:
+!!! note
+ v2.3.0 changed the way datasets are fetched from the knowledge graph.
-## Species
+Datasets are now fetched from the knowledge graph on a region of interest basis.
-The relevant species of datasets catalogued by Knowledge Graph are obtained from the following links:
-
-```json
-{
- "fieldname": "query:species",
- "relative_path": [
- "https://schema.hbp.eu/minds/specimen_group",
- "https://schema.hbp.eu/minds/subjects",
- "https://schema.hbp.eu/minds/species",
- "http://schema.org/name"
- ]
-}
-```
-
-Depending on the selected template space and/or parcellation atlas, the datasets will be filtered to include only datasets from the relevant species.
-
-### Human
-
-If the selected template is any of:
-
-- Big Brain (Histology)
-- MNI Colin 27
-- MNI 152 ICBM 2009c Nonlinear Asymmetric
-
-**or**, the selected parcellation is any of:
-
-- Grey/White matter
-- Cytoarchitectonic Maps
-- BigBrain Cortical Layers Segmentation
-- JuBrain Cytoarchitectonic Atlas
-- Fibre Bundle Atlas - Short Bundle
-- Fibre Bundle Atlas - Long Bundle
-- Cytoarchitectonic Maps
-
-Then datasets which have *`Homo sapiens`* as one of its species described above will proceed to the next filter.
-
-### Rat
-
-And selected parcellation is any of:
-
-- Waxholm Space rat brain atlas v1
-- Waxholm Space rat brain atlas v2
-- Waxholm Space rat brain atlas v3
-
-Then datasets which have *`Rattus norvegicus`* as one of its species described above will proceed to the next filter.
-
-### Mouse
-
-And selected parcellation is any of:
-
-- Allen Mouse Common Coordinate Framework v3 2017
-- Allen Mouse Common Coordinate Framework v3 2015
-
-Then datasets which have *`Mus musculus`* as one of its species described above will proceed to the next filter.
-
-
-## Selected template space and parcellation atlas
-
-The datasets are then filtered based on the selected template space and parcellation atlas.
-
-The dataset may satisfy either conditionals to be presented to the user.
-
-### Template space
-
-The reference space associated with datasets are queried with the following querying links:
-
-```json
-{
- "fieldname": "query:referenceSpaces",
- "fields": [
- {
- "fieldname": "query:name",
- "relative_path": "http://schema.org/name"
- },
- {
- "fieldname": "query:fullId",
- "relative_path": "@id"
- }
- ],
- "relative_path": "https://schema.hbp.eu/minds/reference_space"
-}
-```
-
-The dataset is considered relevant if the stripped `fullId` attribute[^1] of any of the reference spaces matches to:
-
-[^1]: `fullId` is a URI, which in the case of Human Brain Project Knowledge Graph, always starts with `https://nexus.humanbrainproject.org/v0/data/`. Stripping the domain allows for easier comparison.
-
-| Selected template space | fullId |
-| --- | --- |
-| Big Brain (Histology) | minds/core/dataset/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588 |
-| MNI 152 ICBM 2009c Nonlinear Asymmetric | minds/core/dataset/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2 |
-| MNI Colin 27 | minds/core/dataset/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992 |
-
-### Parcellation atlas
-
-The parcellation atlas associated with the dataset are quried with the following querying links:
-
-```json
-{
- "fieldname": "query:parcellationAtlas",
- "fields": [
- {
- "fieldname": "query:name",
- "relative_path": "http://schema.org/name"
- },
- {
- "fieldname": "query:fullId",
- "relative_path": "@id"
- },
- {
- "fieldname": "query:id",
- "relative_path": "http://schema.org/identifier"
- }
- ],
- "relative_path": "https://schema.hbp.eu/minds/parcellationAtlas"
-}
-```
-
-The parcellation region associated with the dataset are queried with the following querying links:
-
-```json
-{
- "fieldname": "query:parcellationRegion",
- "fields": [
- {
- "fieldname": "query:name",
- "relative_path": "http://schema.org/name"
- },
- {
- "fieldname": "query:species",
- "fields": [
- {
- "fieldname": "query:name",
- "relative_path": "http://schema.org/name"
- },
- {
- "fieldname": "query:fullId",
- "relative_path": "@id"
- },
- {
- "fieldname": "query:identifier",
- "relative_path": "http://schema.org/identifier"
- }
- ],
- "relative_path": "https://schema.hbp.eu/minds/species"
- },
- {
- "fieldname": "query:alias",
- "relative_path": "https://schema.hbp.eu/minds/alias"
- }
- ],
- "relative_path": "https://schema.hbp.eu/minds/parcellationRegion"
-}
-```
-
-A dataset is considered relevant if **both** of the following conditionals are true:
-
-#### Parcellation name
-
-If the name of the selected parcellation in interactive atlas viewer matches exactly with either name of any of the `parcellationAtlas`, or any of its aliases listed below
-
-| `parcellationAtlas` name | aliases |
-| --- | --- |
-| Jülich Cytoarchitechtonic Brain Atlas (human) | Cytoarchitectonic Maps |
-| Jülich Cytoarchitechtonic Brain Atlas (human) | JuBrain Cytoarchitectonic Atlas |
-
-!!! important
- If the dataset does not have any `parcellationAtlas` defined, it is considered relevant, and will return `true` for this conditional.
-
-#### Parcellation region
-
-To determine if the dataset is relevant based on the parcellation region, **either one** of the following conditions needs to be met:
-
-- If the fullId of any of the `parcellationRegion` matches any of the fullId of a region described under the selected parcellation
-- If the fullId of any of the `parcellationRegion` matches the fullId of any `relatedAreas` of a region described under the selected parcellation.
-
-For example, the following datasets ...
-
-```json
-{
- "name": "foo",
- "parcellationRegion": [
- {
- "species": [],
- "name": "Area 44d",
- "fullId": "minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052",
- "alias": null
- }
- ]
-}
-
-```
-
-```json
-{
- "name": "bar",
- "parcellationRegion": [
- {
- "species": [],
- "name": "Area 44 (IFG)",
- "fullId": "minds/core/parcellationregion/v1.0.0/8a6be82c-5947-4fff-8348-cf9bf73e4f40",
- "alias": null
- }
- ]
-}
-```
-
-... will be considered relevant to `JuBrain Cytoarchitectonic Atlas`, as it has an region entry with the following attributes:
-
-```json
-
-{
- "name": "Area 44 (IFG)",
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
- }
- },
- "relatedAreas": [
- {
- "name": "Area 44v",
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
- }
- }
- },
- {
- "name": "Area 44d",
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
- }
- }
- }
- ]
-}
-```
\ No newline at end of file
+Currently, only parcellation regions are supported.
diff --git a/docs/releases/v2.3.0.md b/docs/releases/v2.3.0.md
index 732dcb151..76e093344 100644
--- a/docs/releases/v2.3.0.md
+++ b/docs/releases/v2.3.0.md
@@ -13,8 +13,12 @@
- showing contributors to a regional feature/dataset if publications are not available
- added the ability to customize preview origin dataset to labels other to `View probability map`
-# Bugfixes:
+## Bugfixes:
- dataset list view explicitly show loading status
- fixed a few typos
- fixed the reference space name of `ICBM 152 2009c Nonlinear Asymmetric`
+
+# Under the hood stuff
+
+- Updated how dataset retrieval work. It will now query on a region basis
--
GitLab