
# Multi-omics: state of the field

(https://travis-ci.com/krassowski/multi-omics-state-of-the-field)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/multi-omics-state-of-the-field/HEAD?urlpath=lab/tree/notebooks)

Analyses for [State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing](https://doi.org/10.3389/fgene.2020.610798).

## Overview

[![Overview figure - click to go to the PDF version](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.png?raw=true)](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.pdf)

**Figure 1**. Characterization of multi-omics literature based on a systematic screen of PubMed indexed articles (up to July 2020).

The comprehensive search terms (see the online repository for details) were collapsed into four categories;
_integrated omics_ (*) includes _integromics_ and _integrative_ omics,
_multi-view_ (\*\*) includes multi-view|block|source|modal omics,
_other terms_ (\*\*\*) include pan-, trans-, poly-, cross-omics.

The subpanels present:
- A) Combinations of omics (grouped by the characterized entities) commonly discussed occurring together in multi-omics articles (intersections with ≥ 3 omics and at least 50 papers).
The proteins group (1) also includes peptides; the metabolites group (2) includes other endogenous molecules; the epigenetic group (3) encompasses all epigenetic modifications.
- B) Trend plot representing the rapidly increasing number of multi-omics articles indexed in PubMed (also after adjusting for the number of articles published in matched journals - data not shown); the dip in 2020 can be attributed to indexing delay which was not accounted for in the current plot.
- C) Distribution of articles categories that mention different numbers of omics; while it is understandable that multi-omics Reviews category discuss many omics, the Computational method category articles appear to lag behind all other article category types.
The detected number of omics may underestimate the actual numbers (due to the automated search strategy) but should put a useful lower bound on the number of omics discussed.
Bootstrapped 95% confidence intervals around the mean are presented with the whiskers.
- D) The number of articles mentioning the most popular clinical findings, disease terms (here screening is based on ClinVar diseases list) and species (based upon NCBI Taxonomy database).
Both databases were manually filtered down to remove ambiguous terms and merge plural/singular forms.
Only the abstracts were screened here.
- E) The detected references to code, data versioning, distribution platforms and systems (links to repositories with deposited code/data); both the abstracts and full-texts (open-access subset, 44% of all articles) were screened.
No manual curation to classify intent of the link inclusion (i.e. to share authors' code/data vs to report the use of a dataset/tool) was undertaken.

### Methods

PubMed database was searched for articles pertaining to multi-omics on 25th July 2020, using fourteen terms (multi|pan|trans|poly|cross-omics, multi-table|source|view|modal|block omics, integrative omics, integrated omics and integromics) including plural/singular and hyphenated/unhyphenated variants combinations.
The search was automated via Entrez E-utilities API and restricted to Text Words (to avoid matching articles based on the affiliation of authors to companies such as Panomics, Inc. or Integromics S.L.); the full text and additional metadata were retrieved from the PubMed Central (PMC) database for the open access subset of articles.
The feature extraction was performed via n-gram matching against ClinVar (diseases & clinical findings) and NCBI Taxonomy (species) databases, while omics references annotation was based on regular expressions capturing phrases with suffix -ome or -omic (accounting for multi-omic phrases and plural variants).
All matches were manually filtered down to exclude false or irrelevant matches and to merge plural forms.
The article type was collated from five sources:
- MeSH PublicationType as provided by PubMed,
- community-maintained list of multi-omics software packages and methods: [mikelove/awesome-multi-omics](https://github.com/mikelove/awesome-multi-omics),
- PMC-derived:
   -  ArticleType and
   - Subjects (journal-specific);
- manual annotation of articles published in Bioinformatics (Oxford, UK) due to lack of methods subject annotations in PMC data for this journal (performed by MK)

#### Flow diagram

<img src="https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/flowchart.png?raw=true" title="Flowchart with counts" width=500>

**Figure 2**. A flow diagram of the semi-automated multi-omics literature screening effort (up to July 2020).


#### Code overview

[![Overview of the notebooks in the repository](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/repository.svg)](https://raw.githubusercontent.com/krassowski/multi-omics-state-of-the-field/master/figures/repository.svg)

**Figure 3**. Overview of the notebooks in this code repository. Click on the plot to display an interactive version, from where you can open respective notebooks by clicking on the analysis nodes.


### Reference

This analysis was contributed to our [introductory review of multi-omics field](https://doi.org/10.3389/fgene.2020.610798), now published in Frontiers in Genetics (open access):

 Krassowski M, Das V, Sahu SK and Misra BB (2020) State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. Front. Genet. 11:610798. doi: 10.3389/fgene.2020.610798


### Reproducing

Prerequisites:

- Ubuntu: 20.04 (x64)
- Python: 3.8.3
- R: 3.6.3

Install the minimal requirements for reproduction and download required data:

```bash
pip install -r setup/requirements.txt
Rscript helpers/restore.R
cd data
./download.sh
```


### Development and contributing

Install additional requirements for development and testing:

```bash
pip install -r setup/requirements-dev.txt
```

Execute tests with:

```bash
python3 -m pytest
```

Freeze (snapshot) R requirements with:

```bash
Rscript helpers/freeze.R
```

Create the repository overview graph:

```bash
pip install nbpipeline
PYTHONPATH=$(pwd):$PYTHONPATH nbpipeline --dry_run -s -O figures/repository.svg --display_graph_with none
```

	a/README.md		b/README.md
1	# Multi-omics: state of the field	1	# Multi-omics: state of the field
2		2
3	[![Build Status](https://travis-ci.com/krassowski/multi-omics-state-of-the-field.svg?token=JhArfvq99eozHLbsktv8&branch=master)](https://travis-ci.com/krassowski/multi-omics-state-of-the-field)	3	(https://travis-ci.com/krassowski/multi-omics-state-of-the-field)
4	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/multi-omics-state-of-the-field/HEAD?urlpath=lab/tree/notebooks)	4	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/multi-omics-state-of-the-field/HEAD?urlpath=lab/tree/notebooks)
5		5
6	Analyses for [State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing](https://doi.org/10.3389/fgene.2020.610798).	6	Analyses for [State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing](https://doi.org/10.3389/fgene.2020.610798).
7		7
8	## Overview	8	## Overview
9		9
10	[![Overview figure - click to go to the PDF version](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.png?raw=true)](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.pdf)	10	[![Overview figure - click to go to the PDF version](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.png?raw=true)](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/overview.pdf)
11		11
12	Figure 1. Characterization of multi-omics literature based on a systematic screen of PubMed indexed articles (up to July 2020).	12	Figure 1. Characterization of multi-omics literature based on a systematic screen of PubMed indexed articles (up to July 2020).
13		13
14	The comprehensive search terms (see the online repository for details) were collapsed into four categories;	14	The comprehensive search terms (see the online repository for details) were collapsed into four categories;
15	_integrated omics_ (*) includes _integromics_ and _integrative_ omics,	15	_integrated omics_ (*) includes _integromics_ and _integrative_ omics,
16	_multi-view_ (\\) includes multi-view\|block\|source\|modal omics,	16	_multi-view_ (\\) includes multi-view\|block\|source\|modal omics,
17	_other terms_ (\\\*) include pan-, trans-, poly-, cross-omics.	17	_other terms_ (\\\*) include pan-, trans-, poly-, cross-omics.
18		18
19	The subpanels present:	19	The subpanels present:
20	- A) Combinations of omics (grouped by the characterized entities) commonly discussed occurring together in multi-omics articles (intersections with ≥ 3 omics and at least 50 papers).	20	- A) Combinations of omics (grouped by the characterized entities) commonly discussed occurring together in multi-omics articles (intersections with ≥ 3 omics and at least 50 papers).
21	The proteins group (1) also includes peptides; the metabolites group (2) includes other endogenous molecules; the epigenetic group (3) encompasses all epigenetic modifications.	21	The proteins group (1) also includes peptides; the metabolites group (2) includes other endogenous molecules; the epigenetic group (3) encompasses all epigenetic modifications.
22	- B) Trend plot representing the rapidly increasing number of multi-omics articles indexed in PubMed (also after adjusting for the number of articles published in matched journals - data not shown); the dip in 2020 can be attributed to indexing delay which was not accounted for in the current plot.	22	- B) Trend plot representing the rapidly increasing number of multi-omics articles indexed in PubMed (also after adjusting for the number of articles published in matched journals - data not shown); the dip in 2020 can be attributed to indexing delay which was not accounted for in the current plot.
23	- C) Distribution of articles categories that mention different numbers of omics; while it is understandable that multi-omics Reviews category discuss many omics, the Computational method category articles appear to lag behind all other article category types.	23	- C) Distribution of articles categories that mention different numbers of omics; while it is understandable that multi-omics Reviews category discuss many omics, the Computational method category articles appear to lag behind all other article category types.
24	The detected number of omics may underestimate the actual numbers (due to the automated search strategy) but should put a useful lower bound on the number of omics discussed.	24	The detected number of omics may underestimate the actual numbers (due to the automated search strategy) but should put a useful lower bound on the number of omics discussed.
25	Bootstrapped 95% confidence intervals around the mean are presented with the whiskers.	25	Bootstrapped 95% confidence intervals around the mean are presented with the whiskers.
26	- D) The number of articles mentioning the most popular clinical findings, disease terms (here screening is based on ClinVar diseases list) and species (based upon NCBI Taxonomy database).	26	- D) The number of articles mentioning the most popular clinical findings, disease terms (here screening is based on ClinVar diseases list) and species (based upon NCBI Taxonomy database).
27	Both databases were manually filtered down to remove ambiguous terms and merge plural/singular forms.	27	Both databases were manually filtered down to remove ambiguous terms and merge plural/singular forms.
28	Only the abstracts were screened here.	28	Only the abstracts were screened here.
29	- E) The detected references to code, data versioning, distribution platforms and systems (links to repositories with deposited code/data); both the abstracts and full-texts (open-access subset, 44% of all articles) were screened.	29	- E) The detected references to code, data versioning, distribution platforms and systems (links to repositories with deposited code/data); both the abstracts and full-texts (open-access subset, 44% of all articles) were screened.
30	No manual curation to classify intent of the link inclusion (i.e. to share authors' code/data vs to report the use of a dataset/tool) was undertaken.	30	No manual curation to classify intent of the link inclusion (i.e. to share authors' code/data vs to report the use of a dataset/tool) was undertaken.
31		31
32	### Methods	32	### Methods
33		33
34	PubMed database was searched for articles pertaining to multi-omics on 25th July 2020, using fourteen terms (multi\|pan\|trans\|poly\|cross-omics, multi-table\|source\|view\|modal\|block omics, integrative omics, integrated omics and integromics) including plural/singular and hyphenated/unhyphenated variants combinations.	34	PubMed database was searched for articles pertaining to multi-omics on 25th July 2020, using fourteen terms (multi\|pan\|trans\|poly\|cross-omics, multi-table\|source\|view\|modal\|block omics, integrative omics, integrated omics and integromics) including plural/singular and hyphenated/unhyphenated variants combinations.
35	The search was automated via Entrez E-utilities API and restricted to Text Words (to avoid matching articles based on the affiliation of authors to companies such as Panomics, Inc. or Integromics S.L.); the full text and additional metadata were retrieved from the PubMed Central (PMC) database for the open access subset of articles.	35	The search was automated via Entrez E-utilities API and restricted to Text Words (to avoid matching articles based on the affiliation of authors to companies such as Panomics, Inc. or Integromics S.L.); the full text and additional metadata were retrieved from the PubMed Central (PMC) database for the open access subset of articles.
36	The feature extraction was performed via n-gram matching against ClinVar (diseases & clinical findings) and NCBI Taxonomy (species) databases, while omics references annotation was based on regular expressions capturing phrases with suffix -ome or -omic (accounting for multi-omic phrases and plural variants).	36	The feature extraction was performed via n-gram matching against ClinVar (diseases & clinical findings) and NCBI Taxonomy (species) databases, while omics references annotation was based on regular expressions capturing phrases with suffix -ome or -omic (accounting for multi-omic phrases and plural variants).
37	All matches were manually filtered down to exclude false or irrelevant matches and to merge plural forms.	37	All matches were manually filtered down to exclude false or irrelevant matches and to merge plural forms.
38	The article type was collated from five sources:	38	The article type was collated from five sources:
39	- MeSH PublicationType as provided by PubMed,	39	- MeSH PublicationType as provided by PubMed,
40	- community-maintained list of multi-omics software packages and methods: [mikelove/awesome-multi-omics](https://github.com/mikelove/awesome-multi-omics),	40	- community-maintained list of multi-omics software packages and methods: [mikelove/awesome-multi-omics](https://github.com/mikelove/awesome-multi-omics),
41	- PMC-derived:	41	- PMC-derived:
42	- ArticleType and	42	- ArticleType and
43	- Subjects (journal-specific);	43	- Subjects (journal-specific);
44	- manual annotation of articles published in Bioinformatics (Oxford, UK) due to lack of methods subject annotations in PMC data for this journal (performed by MK)	44	- manual annotation of articles published in Bioinformatics (Oxford, UK) due to lack of methods subject annotations in PMC data for this journal (performed by MK)
45		45
46	#### Flow diagram	46	#### Flow diagram
47		47
48	<img src="https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/flowchart.png?raw=true" title="Flowchart with counts" width=500>	48	<img src="https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/flowchart.png?raw=true" title="Flowchart with counts" width=500>
49		49
50	Figure 2. A flow diagram of the semi-automated multi-omics literature screening effort (up to July 2020).	50	Figure 2. A flow diagram of the semi-automated multi-omics literature screening effort (up to July 2020).
51		51
52		52
53	#### Code overview	53	#### Code overview
54		54
55	[![Overview of the notebooks in the repository](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/repository.svg)](https://raw.githubusercontent.com/krassowski/multi-omics-state-of-the-field/master/figures/repository.svg)	55	[![Overview of the notebooks in the repository](https://github.com/krassowski/multi-omics-state-of-the-field/blob/master/figures/repository.svg)](https://raw.githubusercontent.com/krassowski/multi-omics-state-of-the-field/master/figures/repository.svg)
56		56
57	Figure 3. Overview of the notebooks in this code repository. Click on the plot to display an interactive version, from where you can open respective notebooks by clicking on the analysis nodes.	57	Figure 3. Overview of the notebooks in this code repository. Click on the plot to display an interactive version, from where you can open respective notebooks by clicking on the analysis nodes.
58		58
59		59
60	### Reference	60	### Reference
61		61
62	This analysis was contributed to our [introductory review of multi-omics field](https://doi.org/10.3389/fgene.2020.610798), now published in Frontiers in Genetics (open access):	62	This analysis was contributed to our [introductory review of multi-omics field](https://doi.org/10.3389/fgene.2020.610798), now published in Frontiers in Genetics (open access):
63		63
64	> Krassowski M, Das V, Sahu SK and Misra BB (2020) State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. Front. Genet. 11:610798. doi: 10.3389/fgene.2020.610798	64	Krassowski M, Das V, Sahu SK and Misra BB (2020) State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. Front. Genet. 11:610798. doi: 10.3389/fgene.2020.610798
65		65
66		66
67	### Reproducing	67	### Reproducing
68		68
69	Prerequisites:	69	Prerequisites:
70		70
71	- Ubuntu: 20.04 (x64)	71	- Ubuntu: 20.04 (x64)
72	- Python: 3.8.3	72	- Python: 3.8.3
73	- R: 3.6.3	73	- R: 3.6.3
74		74
75	Install the minimal requirements for reproduction and download required data:	75	Install the minimal requirements for reproduction and download required data:
76		76
77	```bash	77	```bash
78	pip install -r setup/requirements.txt	78	pip install -r setup/requirements.txt
79	Rscript helpers/restore.R	79	Rscript helpers/restore.R
80	cd data	80	cd data
81	./download.sh	81	./download.sh
82	```	82	```
83		83
84		84
85	### Development and contributing	85	### Development and contributing
86		86
87	Install additional requirements for development and testing:	87	Install additional requirements for development and testing:
88		88
89	```bash	89	```bash
90	pip install -r setup/requirements-dev.txt	90	pip install -r setup/requirements-dev.txt
91	```	91	```
92		92
93	Execute tests with:	93	Execute tests with:
94		94
95	```bash	95	```bash
96	python3 -m pytest	96	python3 -m pytest
97	```	97	```
98		98
99	Freeze (snapshot) R requirements with:	99	Freeze (snapshot) R requirements with:
100		100
101	```bash	101	```bash
102	Rscript helpers/freeze.R	102	Rscript helpers/freeze.R
103	```	103	```
104		104
105	Create the repository overview graph:	105	Create the repository overview graph:
106		106
107	```bash	107	```bash
108	pip install nbpipeline	108	pip install nbpipeline
109	PYTHONPATH=$(pwd):$PYTHONPATH nbpipeline --dry_run -s -O figures/repository.svg --display_graph_with none	109	PYTHONPATH=$(pwd):$PYTHONPATH nbpipeline --dry_run -s -O figures/repository.svg --display_graph_with none
110	```	110	```