Taxonomy Development Tools
- {% with tdt_version="1.0.6" %}
+ {% with tdt_version="1.0.7" %}
{% if tdt_version %}
v{{ tdt_version }}
{% endif %}
{% endwith %}
diff --git a/src/resources/table.html b/src/resources/table.html
index adb55e4..8f0b566 100644
--- a/src/resources/table.html
+++ b/src/resources/table.html
@@ -539,11 +539,13 @@
{{ value.label or name
// generate at string per accession and store in all_ats
for (var row_index in at_data) {
var row = at_data[row_index];
- source_taxonomy = row["source_taxonomy"].split("/").at(-1).split(".")[0];
- transferred_cell_label = row["transferred_cell_label"];
- ats = all_ats[row["target_node_accession"]] || [];
- ats.push(source_taxonomy + ": " + transferred_cell_label);
- all_ats[row["target_node_accession"]] = ats;
+ if (row["source_taxonomy"]) {
+ source_taxonomy = row["source_taxonomy"].split("/").at(-1).split(".")[0];
+ transferred_cell_label = row["transferred_cell_label"];
+ ats = all_ats[row["target_node_accession"]] || [];
+ ats.push(source_taxonomy + ": " + transferred_cell_label);
+ all_ats[row["target_node_accession"]] = ats;
+ }
}
$.each(all_ats, (key, val) => {
var at_cell = $("a[name='at_" + key + "']");
diff --git a/src/schema/column.tsv b/src/schema/column.tsv
index a19cd22..07bd775 100644
--- a/src/schema/column.tsv
+++ b/src/schema/column.tsv
@@ -22,14 +22,14 @@ datatype HTML type empty html_type the HTML type for viewing and editing this
annotation cell_set_accession cell set accession text primary An identifier that can be used to consistently refer to the set of cells being annotated, even if the cell_label changes.
annotation cell_label cell label empty text This denotes any free-text term which the author uses to annotate cells, i.e. the preferred cell label name used by the author. Abbreviations are exceptable in this field; refer to 'cell_fullname' for related details. Certain key words have been reserved: - `'doublets'` is reserved for encoding cells defined as doublets based on some computational analysis - `'junk'` is reserved for encoding cells that failed sequencing for some reason, e.g. few genes detected, high fraction of mitochondrial reads - `'unknown'` is explicitly reserved for unknown or 'author does not know' - `'NA'` is incomplete, i.e. no cell annotation was provided
annotation cell_fullname cell fullname empty text This MUST be the full-length name for the biological entity listed in `cell_label` by the author. (If the value in `cell_label` is the full-length term, this field will contain the same value.) NOTE: any reserved word used in the field 'cell_label' MUST match the value of this field. EXAMPLE 1: Given the matching terms 'LC' and 'luminal cell' used to annotate the same cell(s), then users could use either terms as values in the field 'cell_label'. However, the abbreviation 'LC' CANNOT be provided in the field 'cell_fullname'. EXAMPLE 2: Either the abbreviation 'AC' or the full-length term intended by the author 'GABAergic amacrine cell' MAY be placed in the field 'cell_label', but as full-length term naming this biological entity, 'GABAergic amacrine cell' MUST be placed in the field 'cell_fullname'.
-annotation parent_cell_set_accession parent cell set accession empty text
+annotation parent_cell_set_accession parent cell set accession empty text A list of accessions of cell sets that subsume this cell set. This can be used to compose hierarchies of annotated cell sets, built from a fixed set of clusters.
annotation parent_cell_set_name parent cell set name empty text
annotation labelset labelset empty text from(labelset.name) The unique name of the set of cell annotations. Each cell within the AnnData/Seurat file MUST be associated with a 'cell_label' value in order for this to be a valid 'cellannotation_setname'.
annotation cell_ontology_term_id cell ontology term id empty autocomplete_cl This MUST be a term from either the Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/cl) or from some ontology that extends it by classifying cell types under terms from the Cell Ontology e.g. the Provisional Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/pcl) or the Drosophila Anatomy Ontology (DAO) (https://www.ebi.ac.uk/ols4/ontologies/fbbt). NOTE: The closest available ontology term matching the value within the field 'cell_label' (at the time of publication) MUST be used. For example, if the value of 'cell_label' is 'relay interneuron', but this entity does not yet exist in the ontology, users must choose the closest available term in the CL ontology. In this case, it's the broader term 'interneuron' i.e. https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:0000099.
annotation cell_ontology_term cell ontology term empty ontology_label This MUST be the human-readable name assigned to the value of 'cell_ontology_term_id'
annotation rationale rationale empty text The free-text rationale which users provide as justification/evidence for their cell annotations. Researchers are encouraged to use this field to cite relevant publications in-line using standard academic citations of the form `(Zheng et al., 2020)` This human-readable free-text MUST be encoded as a single string. All references cited SHOULD be listed using DOIs under rationale_dois. There MUST be a 2000-character limit.
annotation rationale_dois rationale dois empty text A list of valid publication DOIs cited by the author to support or provide justification/evidence/context for 'cell_label'. Multiple values can be concatenated by using the '|' character as a delimiter.
-annotation marker_gene_evidence marker gene evidence empty text List of gene names explicitly used as evidence for this cell annotation. Each gene MUST be included in the matrix of the AnnData/Seurat file. Multiple values can be concatenated by using the '|' character as a delimiter.
+annotation marker_gene_evidence marker gene evidence empty text List of names of genes whose expression in the cells being annotated is explicitly used as evidence for this cell annotation. Each gene MUST be included in the matrix of the AnnData/Seurat file. Multiple values can be concatenated by using the '|' character as a delimiter.
annotation synonyms synonyms empty text This field denotes any free-text term of a biological entity which the author associates as synonymous with the biological entity listed in the field 'cell_label'. In the case whereby no synonyms exist, the authors MAY leave this as blank, which is encoded as 'NA'. However, this field is NOT OPTIONAL. Multiple values can be concatenated by using the '|' character as a delimiter.
labelset name name text primary
labelset description description empty text Some text describing what types of cell annotation this annotation key is used to record
@@ -40,13 +40,13 @@ labelset automated_annotation_algorithm_version automated annotation algorithm v
labelset automated_annotation_algorithm_repo_url automated annotation algorithm repo url empty text This field denotes the URL of the version control repository associated with the algorithm used (if applicable). It MUST be a string of a valid URL.
labelset automated_annotation_reference_location automated annotation reference location empty text This field denotes a valid URL of the annotated dataset that was the source of annotated reference data. This MUST be a string of a valid URL. The concept of a 'reference' specifically refers to 'annotation transfer' algorithms, whereby a 'reference' dataset is used to transfer cell annotations to the 'query' dataset.
metadata index index text primary
-metadata author_name author name empty text This MUST be a string in the format `[FIRST NAME] [LAST NAME]`
-metadata author_contact author contact empty text This MUST be a valid email address of the author
-metadata orcid orcid empty text This MUST be a valid ORCID for the author
-metadata author_list author list empty text
+metadata author_name author name empty text Primary author's name. This MUST be a string in the format `[FIRST NAME] [LAST NAME]`
+metadata author_contact author contact empty text Primary author's contact. This MUST be a valid email address of the author
+metadata orcid orcid empty text Primary author's orcid. This MUST be a valid ORCID for the author
+metadata author_list author list empty text This field stores a list of users who are included in the project as collaborators, regardless of their specific role. An example list; '['John Smith', 'Cody Miller', 'Sarah Jones']'
metadata matrix_file_id matrix file id empty text A resolvable ID for a cell by gene matrix file in the form namespace:accession, e.g. CellXGene_dataset:8e10f1c4-8e98-41e5-b65f-8cd89a887122. Please see https://github.com/cellannotation/cell-annotation-schema/registry/registry.json for supported namespaces.
-metadata title title empty text
-metadata description description empty text
+metadata title title empty text The title of the dataset. This MUST be less than or equal to 200 characters. e.g. 'Human retina cell atlas - retinal ganglion cells'.
+metadata description description empty text The description of the dataset. e.g. 'A total of 15 retinal ganglion cell clusters were identified from over 99K retinal ganglion cell nuclei in the current atlas. Utilizing previous characterized markers from macaque, 5 clusters can be annotated.'
metadata cellannotation_schema_version cellannotation schema version empty text The schema version, the cell annotation open standard. Current version MUST follow 0.1.0 This versioning MUST follow the format `'[MAJOR].[MINOR].[PATCH]'` as defined by Semantic Versioning 2.0.0, https://semver.org/
metadata cellannotation_timestamp cellannotation timestamp empty text The timestamp of all cell annotations published (per dataset). This MUST be a string in the format `'%yyyy-%mm-%dd %hh:%mm:%ss'`
metadata cellannotation_version cellannotation version empty text The version for all cell annotations published (per dataset). This MUST be a string. The recommended versioning format is `'[MAJOR].[MINOR].[PATCH]'` as defined by Semantic Versioning 2.0.0, https://semver.org/