POCT v1.0 Release note

1. Tissue-based classification system

The Tissue tree is primarily based on studies of the dicot model plant Arabidopsis and the monocot model plant rice, integrated with single-cell studies and textbook descriptions of other species such as maize, wheat, poplar, and orchids. This classification system starts with organs such as roots, stems, leaves, flowers, inflorescences, and seeds, and is refined based on anatomical knowledge to specific cell types such as epidermis and cortex.

1.1 Metadata overview

Item	Quantity
Reference Species	14
Total Records	967
Tissue Records	7
Cell Type Records	959
Other Records	11
Maximum Classification Levels	10

Reference Species: Includes literature from 14 species: Arabidopsis, cabbage, wild strawberry, soybean, upland cotton, duckweed, cassava, alfalfa, Nepeta cataria, rice, Phalaenopsis, poplar, tomato, and maize.

Total Records: Number of paths.

Maximum Classification Levels: Maximum path length.

1.2 Terminology sources

All cell type terms are sourced from multiple resources:

• Cell type annotation results from the PlantscRNAdb database. Reference literature (DOI Info) for each species can be viewed on the Download page. Example link: http://ibi.zju.edu.cn/plantscrnadb/download/ara_doi_v3.txt
• Cell type annotation results from the scPlantDB database. On the Marker page, click [Table showing all markers to this species] to download all marker genes for a species, including cell types. Example link: https://biobigdata.nju.edu.cn/scplantdb/static/marker_table/arabidopsis_thaliana.marker_fd.csv.gz
• All cell type terms under the native plant cell (PO:0025606) in the Plant Ontology database. Extraction code is provided in the appendix (not detailed here as the appendix is not specified).
• Botany, edited by Fu Chengxin and Ding Bingyang.
• Additional sources listed in the references.

2. Cell-type-based classification system

The Cell type tree groups cell type terms from the Tissue Tree based on their cellular identity and constructs a hierarchical tree. The first level represents cellular identity, while the second and subsequent levels correspond to specific cell type terms from the Tissue Tree. Currently, 158 cellular identities have been identified.

2.1 Metadata overview

Item	Quantity
Cell Type Records	234
Maximum Levels	5

Cell Type Records: Number of Tissue Tree paths involved in the Cell Type Tree.

Maximum Levels: Deepest level of the Cell Type Tree.

2.2 Terminology naming

Cell type terms in this classification system are derived by adding prefixes and suffixes to terms from the Tissue Tree. The rules are as follows:

• Organ-specific cell types directly use the Tissue Tree terms. For example, Anther cap (PCTO:00000001) (specific to flowers/inflorescences) is used as is in the Cell Type Tree.
• For mature and differentiated cell types shared in multiple organs and tissues, the common part are extracted from those cell types in Tissue Tree. For example, Abaxial epidermis (PCTO:00000039) is extracted from Sepal abaxial epidermis (PO:0006054), Petal abaxial epidermis (PO:0006052), Tepal abaxial epidermis (PO:0025192) and similar entities.
• For cell types in early or intermediate differentiation stages present in multiple organs, terms are adjusted to reflect their subsequent fate in the next level. For example, initial cell terms are prefixed to indicate their future cell type, such as Lateral root initial cell, Stem cortex - endodermis initial cell, or Stomatal initial cell.

3. References

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