1 Introduction

The ambitions of collaborative single cell biology will only be achieved through the coordinated efforts of many groups, to help clarify cell types and dynamics in an array of functional and environmental contexts. The use of formal ontology in this pursuit is well-motivated and research progress has already been substantial.

Bakken et al. (2017) discuss “strategies for standardized cell type representations based on the data outputs from [high-content flow cytometry and single cell RNA sequencing], including ‘context annotations’ in the form of standardized experiment metadata about the specimen source analyzed and marker genes that serve as the most useful features in machine learning-based cell type classification models.” Aevermann et al. (2018) describe how the FAIR principles can be implemented using statistical identification of necessary and sufficient conditions for determining cell class membership. They propose that Cell Ontology can be transformed to a broadly usable knowledgebase through the incorporation of accurate marker gene signatures for cell classes.

In this vignette, we review key concepts and tasks required to make progress in the adoption and application of ontological discipline in Bioconductor-oriented data analysis.

2 Scope of package

The following table describes the resources available with get* commands defined in ontoProc.

X func purpose nclass nprop nroots datav fmtv
1 getCellLineOnto Cell line catalog 41780 6 18 NA NA
2 getCellOnto Cell biology concepts 6708 59 38 releases/2018-07-07 1.2
3 getCellosaurusOnto Cell line concepts 87311 6 87311 23 1.2
4 getChebiLite Chemicals of biological interest 108496 6 12 155 1.2
5 getChebiOnto 108496 33 12 155 1.2
6 getDiseaseOnto Human disease 11283 24 13 releases/2018-06-29 1.2
7 getEFOOnto Experimental factors 20115 6 36 2.87 1.2
8 getGeneOnto Gene ontology 47123 43 10 releases/2018-03-27 1.2
9 getHCAOnto Human cell atlas 11047 6 76 NA NA
10 getOncotreeOnto Tumor relations 1298 15 3 ncit/releases/2017-12-15/ncit-oncotree.ttl 1.2
11 getPATOnto Phenotypes and traits 2670 43 21 releases/2018-11-12 1.2
12 getPROnto Protein ontology 315957 6 53 57 1.2
13 getUBERON_NE Anatomy 14937 6 135 releases/2017-09-09 1.2

3 Methods

3.1 Conceptual overview of ontology with cell types

Definitions, semantics. For concreteness, we provide some definitions and examples. We use ontology to denote the systematic organization of terminology used in a conceptual domain. The Cell Ontology is a graphical data structure with carefully annotated terms as nodes and conventionally defined semantic relationships among terms serving as edges. As an example, lung ciliated cell has URI . This URI includes a fixed-length identifier CL_1000271 with unambiguous interpretation wherever it is encountered. There is a chain of relationships from lung ciliated cell up through ciliated cell, then native cell, then cell, each possessing its own URI and related interpretive metadata. The relationship connecting the more precise to the less precise term in this chain is denoted SubclassOf. Ciliated cell is equivalent to a native cell that has plasma membrane part cilium. Semantic characteristics of terms and relationships are used to infer relationships among terms that may not have relations directly specified in available ontologies.

Barriers to broad adoption. Given the wealth of material available in biological ontologies, it is somewhat surprising that formal annotation is so seldom used in practice. Barriers to more common use of ontology in data annotation include: (i) Non-existence of exact matching between intended term and terms available in ontologies of interest. (ii) The practical problem of decoding ontology identifiers. A GO tag or CL tag is excellent for programming, but it is clumsy to co-locate with the tag the associated natural language term or phrase. (iii) Likelihood of disagreement of suitability of terms for conditions observed at the boundaries of knowledge. To help cope with the first of these problems, Bioconductor’s ontologyProc package includes a function liberalMap which will search an ontology for terms lexically close to some target term or phrase. The second problem can be addressed with more elaborate data structures for variable annotation and programming in R, and the third problem will diminish in importance as the value of ontology adoption becomes manifest in more applications.

Class vs. instance. It is important to distinguish the practice of designing and maintaining ontologies from the use of ontological class terms to annotate instances of the concepts. The combination of an ontology and a set of annotated instances is called a knowledge base. To illustrate some of the salient distinctions here, consider the cell line called A549, which is established from a human lung adenocarcinoma sample. There is no mention of A549 in the Cell Ontology. However, A549 is present in the EBI Experimental Factor Ontology as a subclass of the “Homo sapiens cell line” class. Presumably this is because A549 is a class of cells that are widely used experimentally, and this cell line constitutes a concept deserving of mapping in the universe of experimental factors. In the universe of concepts related to cell structure and function per se, A549 is an individual that can be characterized through possession of or lack of properties enumerated in Cell Ontology, but it is not deserving of inclusion in that ontology.

3.2 Illustration in a single-cell RNA-seq dataset

The 10X Genomics corporation has distributed a dataset on results of sequencing 10000 PBMC from a healthy donor . Subsets of the data are used in tutorials for the Seurat analytical suite (Butler et al. (2018)).

3.2.1 Labeling PBMC in the Seurat tutorial

One result of the tutorial analysis of the 3000 cell subset is a table of cell types and expression-based markers of cell identity. The first three columns of the table below are from concluding material in the Seurat tutorial; the remaining columns are created by “manual” matching between the Seurat terms and terms found in Cell Ontology.

grp markers seurTutType formal tag
0 IL7R CD4 T cells CD4-positive helper T cell CL:0000492
1 CD14, LYZ CD14+ Monocytes CD14-positive monocyte CL:0001054
2 MS4A1 B cells B cell CL:0000236
3 CD8A CD8 T cells CD8-positive, alpha-beta T cell CL:0000625
4 FCGR3A, MS4A7 FCGR3A+ Monocytes monocyte CL:0000576
5 GNLY, NKG7 NK cells natural killer cell CL:0000623
6 FCER1A, CST3 Dendritic Cells dendritic cell CL:0000451
7 PPBP Megakaryocytes megakaryocyte CL:0000556

3.2.2 Relationships asserted in the Cell Ontology

Given the informally selected tags in the table above, we can sketch the Cell Ontology graph connecting the associated cell types. The ontoProc package adds functionality to ontologyPlot with make_graphNEL_from_ontology_plot. This allows use of all Rgraphviz and igraph visualization facilities for graphs derived from ontology structures.

Here we display the PBMC cell sets reported in the Seurat tutorial.

3.2.3 Molecular features asserted in the Cell Ontology

The CLfeats function traces relationships and properties from a given Cell Ontology class. Briefly, each class can assert that it is the intersection_of other classes, and has_part, lacks_part, has_plasma_membrane_part, lacks_plasma_membrane_part can be asserted as relationships holding between cell type instances and cell components. The components are often cross-referenced to Protein Ontology or Gene Ontology. When the Protein Ontology component has a synonym for which an HGNC symbol is provided, that symbol is retrieved by CLfeats. Here we obtain the listing for a mature CD1a-positive dermal dendritic cell.

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded
## no recognized predicate references for CL:0000738
## no recognized predicate references for CL:0000988
## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded
## no recognized predicate references for CL:0000766
## no recognized predicate references for CL:0000219
## no recognized predicate references for CL:0000003
## no recognized predicate references for CL:0000000
tag prtag cond entity SYMBOL name
1 CL:0002531 PR:000001310 hasPMP CD83 molecule CD83 mature CD1a-positive dermal dendritic cell
2 CL:0002531 GO:0042613 hiPMAmt MHC class II protein complex NA mature CD1a-positive dermal dendritic cell
3 CL:0002531 PR:000001412 hiPMAmt CD86 molecule CD86 mature CD1a-positive dermal dendritic cell
4 CL:0002531 PR:000001438 hiPMAmt CD80 molecule CD80 mature CD1a-positive dermal dendritic cell
CL:0002529 CL:0002529 PR:000002025 hasPMP T-cell surface glycoprotein CD1a CD1A CD1a-positive dermal dendritic cell
11 CL:0001006 PR:000001012 hasPMP integrin alpha-M ITGAM dermal dendritic cell
21 CL:0001006 PR:000001026 hasPMP lymphocyte antigen 75 LY75 dermal dendritic cell
31 CL:0001006 PR:000001084 hasPMP T-cell surface glycoprotein CD8 alpha chain CD8A dermal dendritic cell
CL:0000990 CL:0000990 PR:000001013 hiPMAmt integrin alpha-X ITGAX conventional dendritic cell
12 CL:0000451 PR:000001002 lacksPMP CD19 molecule CD19 dendritic cell
22 CL:0000451 PR:000001003 lacksPMP CD34 molecule CD34 dendritic cell
32 CL:0000451 PR:000001020 lacksPMP CD3 epsilon CD3E dendritic cell
41 CL:0000451 PR:000001024 lacksPMP neural cell adhesion molecule 1 NCAM1 dendritic cell
5 CL:0000451 PR:000001289 lacksPMP membrane-spanning 4-domains subfamily A member 1 MS4A1 dendritic cell
6 CL:0000451 GO:0042613 hasPart MHC class II protein complex NA dendritic cell
13 CL:0001010 PR:000001310 hasPMP CD83 molecule CD83 mature dermal dendritic cell
23 CL:0001010 GO:0042613 hiPMAmt MHC class II protein complex NA mature dermal dendritic cell
33 CL:0001010 PR:000001412 hiPMAmt CD86 molecule CD86 mature dermal dendritic cell
42 CL:0001010 PR:000001438 hiPMAmt CD80 molecule CD80 mature dermal dendritic cell
14 CL:0000841 PR:000001310 hasPMP CD83 molecule CD83 mature conventional dendritic cell
24 CL:0000841 GO:0042613 hiPMAmt MHC class II protein complex NA mature conventional dendritic cell
34 CL:0000841 PR:000001412 hiPMAmt CD86 molecule CD86 mature conventional dendritic cell
43 CL:0000841 PR:000001438 hiPMAmt CD80 molecule CD80 mature conventional dendritic cell

The ctmarks function starts a shiny app that generates tables of this sort for selected cell types.

ctmarks snapshot

ctmarks snapshot

3.2.4 Mapping from gene ‘presence/role’ to cell type

The sym2CellOnto function helps find mention of given gene symbols in properties or parts of cell types.

sym cond cl type
ITGAM hasPMP CL:0000040 monoblast
ITGAM hasPMP CL:0000094 granulocyte
ITGAM hasPMP CL:0000129 microglial cell
ITGAM hasPMP CL:0000559 promonocyte
ITGAM hasPMP CL:0000560 band form neutrophil
ITGAM hasPMP CL:0000580 neutrophilic myelocyte
ITGAM hasPMP CL:0000582 neutrophilic metamyelocyte
ITGAM hasPMP CL:0000612 eosinophilic myelocyte
ITGAM hasPMP CL:0000614 basophilic myelocyte
ITGAM hasPMP CL:0000769 basophilic metamyelocyte
ITGAM hasPMP CL:0000773 eosinophilic metamyelocyte
ITGAM hasPMP CL:0000861 elicited macrophage
ITGAM hasPMP CL:0000889 myeloid suppressor cell
ITGAM hasPMP CL:0001006 dermal dendritic cell
ITGAM hasPMP CL:0001007 interstitial dendritic cell
ITGAM hasPMP CL:0001022 CD115-positive monocyte
ITGAM hasPMP CL:0002058 Gr1-low non-classical monocyte
ITGAM hasPMP CL:0002395 Gr1-high classical monocyte
ITGAM hasPMP CL:0002398 Gr1-positive, CD43-positive monocyte
ITGAM hasPMP CL:0002426 CD11b-positive, CD27-positive natural killer cell
ITGAM hasPMP CL:0002457 epidermal Langerhans cell
ITGAM hasPMP CL:0002459 langerin-negative dermal dendritic cell
ITGAM hasPMP CL:0002465 CD11b-positive dendritic cell
ITGAM hasPMP CL:0011114 segmented neutrophil of bone marrow
ITGAM lacksPMP CL:0000037 hematopoietic stem cell
ITGAM lacksPMP CL:0000547 proerythroblast
ITGAM lacksPMP CL:0000553 megakaryocyte progenitor cell
ITGAM lacksPMP CL:0000558 reticulocyte
ITGAM lacksPMP CL:0000611 eosinophil progenitor cell
ITGAM lacksPMP CL:0000613 basophil progenitor cell
ITGAM lacksPMP CL:0000765 erythroblast
ITGAM lacksPMP CL:0000831 mast cell progenitor
ITGAM lacksPMP CL:0000836 promyelocyte
ITGAM lacksPMP CL:0000837 hematopoietic multipotent progenitor cell
ITGAM lacksPMP CL:0000872 splenic marginal zone macrophage
ITGAM lacksPMP CL:0000941 thymic conventional dendritic cell
ITGAM lacksPMP CL:0000942 thymic plasmacytoid dendritic cell
ITGAM lacksPMP CL:0000989 CD11c-low plasmacytoid dendritic cell
ITGAM lacksPMP CL:0000998 CD8_alpha-negative CD11b-negative dendritic cell
ITGAM lacksPMP CL:0001000 CD8_alpha-positive CD11b-negative dendritic cell
ITGAM lacksPMP CL:0001029 common dendritic progenitor
ITGAM lacksPMP CL:0001060 hematopoietic oligopotent progenitor cell, lineage-negative
ITGAM lacksPMP CL:0001066 erythroid progenitor cell, mammalian
ITGAM lacksPMP CL:0002010 pre-conventional dendritic cell
ITGAM lacksPMP CL:0002089 group 2 innate lymphoid cell, mouse
ITGAM lacksPMP CL:0002458 langerin-positive dermal dendritic cell
ITGAM lacksPMP CL:0002679 natural helper lymphocyte
ITGAM hiPMAmt CL:0000581 peritoneal macrophage
ITGAM hiPMAmt CL:0002347 CD27-high, CD11b-high natural killer cell
ITGAM hiPMAmt CL:0002348 CD27-low, CD11b-high natural killer cell
ITGAM hiPMAmt CL:0002474 lymphoid MHC-II-negative classical monocyte
ITGAM hiPMAmt CL:0002475 lymphoid MHC-II-negative non-classical monocyte
ITGAM hiPMAmt CL:0002505 liver CD103-negative dendritic cell
ITGAM hiPMAmt CL:0002510 CD103-negative, langerin-positive lymph node dendritic cell
ITGAM hiPMAmt CL:0002512 CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell
ITGAM loPMAmt CL:0000091 Kupffer cell
ITGAM loPMAmt CL:0000583 alveolar macrophage
ITGAM loPMAmt CL:0000868 lymph node macrophage
ITGAM loPMAmt CL:0000874 splenic red pulp macrophage
ITGAM loPMAmt CL:0002345 CD27-low, CD11b-low immature natural killer cell
ITGAM loPMAmt CL:0002349 CD27-high, CD11b-low natural killer cell
ITGAM loPMAmt CL:0002506 liver CD103-positive dendritic cell
ITGAM loPMAmt CL:0002509 CD103-positive, langerin-positive lymph node dendritic cell
ITGAM loPMAmt CL:0002511 CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell
##   hasPMP lacksPMP  hiPMAmt  loPMAmt 
##       24       23        8        9
sym cond cl type
FOXP3 hasPart CL:0000902 induced T-regulatory cell
FOXP3 hasPart CL:0000903 natural T-regulatory cell
FOXP3 hasPart CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell
FOXP3 hasPart CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell

3.3 Adding terms to ontology_index structures to ‘extend’ Cell Ontology

The task of extending an ontology is partly bureaucratic in nature and depends on a collection of endorsements and updates to centralized information structures. In order to permit experimentation with interfaces and new content that may be quite speculative, we include an approach to combining new ontology ‘terms’ of structure similar to those endorsed in Cell Ontology, to ontologyIndex-based ontology_index instances.

3.3.1 Use case: a set of cell types defined by “diagonal expression”

For a demonstration, we consider the discussion in Bakken et al. (2017), of a ‘diagonal’ expression pattern defining a group of novel cell types. A set of genes is identified and cells are distinguised by expressing exactly one gene from the set.