9691071


Genome Warehouse: A Public Repository Housing 1 

Genome-scale Data 2 

 3 

Meili Chen1,2,#, Yingke Ma1,2,#, Song Wu1,2,3, Xinchang Zheng1,2, Hongen Kang1,2,3, 4 

Jian Sang1,2,3,
†
, Xingjian Xu1,2,3,

††
, Lili Hao1,2, Zhaohua Li1,2,3, Zheng Gong1,2,3, Jingfa 5 

Xiao1,2,3, Zhang Zhang1,2,3, Wenming Zhao1,2,3, Yiming Bao1,2,3,* 6 

1 National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of 7 

Sciences / China National Center for Bioinformation, Beijing 100101, China 8 

2 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of 9 

Genomics, Chinese Academy of Sciences, Beijing 100101, China 10 

3 University of Chinese Academy of Sciences, Beijing 100049, China 11 

 12 

# Equal contribution. 13 

* Corresponding author. 14 

E-mail: baoym@big.ac.cn (Bao Y). 15 

†
 Current address: Division of Cancer Epidemiology and Genetics, National Cancer 16 

Institute, National Institutes of Health, Bethesda, Maryland 20892, USA 17 

† †
 Current address: College of Computer Science Technology, Inner Mongolia 18 

Normal University, Hohhot, Inner Mongolia 010010, China 19 

 20 

Running title: Chen M et al / Genome Assembly Data Repository 21 

 22 

Total letter counts (Title): 63 23 

Total letter counts (Running title): 46 24 

Total word counts (Abstract): 193 25 

Total keywords: 5 26 

Total word counts (from “Introduction” to “Conclusions” or “Materials and 27 

methods”): 1799 28 

Total figures: 3 29 

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Total tables: 1 30 

Total supplementary figures: 0 31 

Total supplementary tables: 0 32 

Total supplementary files: 0 33 

 34 

35 

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Abstract 36 

The Genome Warehouse (GWH) is a public repository housing genome assembly data 37 

for a wide range of species and delivering a series of web services for genome data 38 

submission, storage, release, and sharing. As one of the core resources in the National 39 

Genomics Data Center (NGDC), part of the China National Center for Bioinformation 40 

(CNCB, https://bigd.big.ac.cn/), GWH accepts both full genome and partial genome 41 

(chloroplast, mitochondrion, and plasmid) sequences with different assembly levels, 42 

as well as an update of existing genome assemblies. For each assembly, GWH collects 43 

detailed genome-related metadata including biological project and sample, and 44 

genome assembly information, in addition to genome sequence and annotation. To 45 

archive high-quality genome sequences and annotations, GWH is equipped with a 46 

uniform and standardized procedure for quality control. Besides basic browse and 47 

search functionalities, all released genome sequences and annotations can be 48 

visualized with JBrowse. By December 2020, GWH has received 17,264 direct 49 

submissions covering a diversity of 949 species, and has released 3370 of them. 50 

Collectively, GWH serves as an important resource for genome-scale data 51 

management and provides free and publicly accessible data to support research 52 

activities throughout the world. GWH is publicly accessible at 53 

https://bigd.big.ac.cn/gwh/. 54 

 55 

KEYWORDS: Genome submission; Genome sequence; Genome annotation; 56 

Genome warehouse; Quality control 57 

  58 

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Introduction 59 

Genome sequences and annotations are fundamental information for a wide range of 60 

genome-related studies, including various omics data analysis such as genome [1], 61 

transcriptome [2], epigenome [3,4], and genome variation [5,6]. China, as one of the 62 

most biodiverse countries in the world, harbors more than 10% of the world’s known 63 

species [7]. In the past decades, a large number of genome assemblies of featured and 64 

important animals and crops in China have been sequenced [1, 8–11], most of which 65 

were submitted to International Nucleotide Sequence Database Collaboration (INSDC) 66 

members (National Center for Biotechnology Information (NCBI), European 67 

Bioinformatics Institute (EBI), and DNA Data Bank of Japan (DDBJ)) [12]. With the 68 

rapid growth of genome assembly data, in China for example, large genome data size, 69 

slow data transfer rate due to limited international network transfer bandwidth, and 70 

language barrier for communication of technical issues have obstructed researchers 71 

from efficiently submitting their data to INSDC members. All these call for a 72 

centralized genomic data repository within China to complement the INSDC. 73 

Here, we report the Genome Warehouse (GWH, https://bigd.big.ac.cn/gwh/), a 74 

centralized resource housing genome assembly data and delivering a series of genome 75 

data services. As one of the core resources in the National Genomics Data Center 76 

(NGDC), part of the China National Center for Bioinformation (CNCB, 77 

https://bigd.big.ac.cn/) [13], the aim of GWH is to accept data submissions worldwide 78 

and provide an important resource for genome data quality control, data archive, rapid 79 

release, and public sharing (e.g., with INSDC) in support of research activities from 80 

all over the world. To date, GWH has received a total of 12,366 genome submissions 81 

(including 14 international submissions), demonstrating its increasingly important role 82 

in global genome data management and sharing. 83 

Data model 84 

Designed for compatibility with the INSDC data model, each genome assembly in 85 

GWH is linked to a BioProject (https://bigd.big.ac.cn/bioproject) and a BioSample 86 

(https://bigd.big.ac.cn/biosample), which are two fundamental resources for metadata 87 

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description in CNCB-NGDC. Full or partial (chloroplast, mitochondrion, and plasmid) 88 

genome assemblies with different assembly levels (complete, draft in chromosome, 89 

scaffold, and contig) are all acceptable and existing genome assemblies are allowed to 90 

be updated. Accession numbers are assigned with the following rules (Figure 1): (1) 91 

each genome assembly has an accession number prefixed with "GWH", followed by 92 

four capital letters and eight zeros (e.g., GWHAAAA00000000); (2) genome 93 

sequences have the same accession number format as their corresponding genome 94 

assembly, with the exception that the eight digits start from 00000001 and increase in 95 

order (e.g., GWHAAAA00000001); (3) genes have similar accession pattern as those 96 

of genome sequences, with the addition of letter “G” between the GWH prefix and the 97 

four capital letters, and there are six digits at the end instead of eight (e.g., 98 

GWHGAAAA000001); (4) transcripts use the letter “T” to replace “G” in accession 99 

numbers for genes (e.g., GWHTAAAA000001); (5) proteins use the letter “P” to 100 

replace “G” in accession numbers for genes (e.g., GWHPAAAA000001); (6) if the 101 

submission is an update of existing submission in GWH, it will be assigned a dot and 102 

an incremental number to represent the version (e.g., GWHAAAA00000000.1). 103 

Database components 104 

GWH is a centralized resource housing genome-scale data, with the purpose to 105 

archive high-quality genome sequences and annotation information. GWH is 106 

equipped with a series of web services for genome data submission, release, and 107 

sharing, accordingly involving three major components, namely, data submission, 108 

quality control, and archive and release (Figure 2). 109 

Data submission 110 

GWH not only accepts genome assembly associated data through an on-line 111 

submission system but also allows off-line batch submissions. Users need to register 112 

first and then to provide complete description on submitted genome sequences. 113 

Biological project and sample information should be provided (through BioProject 114 

and BioSample, respectively) together with genome assembly sequence, annotation, 115 

and associated metadata. Metadata mainly consist of a variety of information about 116 

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submitter, general assembly, file(s), sequence assignment, and publication (if 117 

available). After submission, GWH runs an automated quality control pipeline to 118 

check the validity and consistency of submitted genome sequence and genome 119 

annotation files. Accession numbers are assigned to assemblies and sequences upon 120 

the pass of quality control. The updated assembly data can also be submitted to GWH. 121 

It should be noted that compatible with the INSDC members (e.g., NCBI GenBank), it 122 

is the responsibility of the submitters to ensure the data quality, completeness, and 123 

consistency and GWH does not warrant or assume any legal liability or responsibility 124 

for the data accuracy. 125 

Quality control 126 

After metadata and file(s) are received, GWH automatically runs standardized quality 127 

control (QC) to check 45 different types of errors in submitted genome sequences and 128 

annotations, and to scan for contaminated genome sequences (see details at 129 

https://bigd.big.ac.cn/gwh/documents) if needed (Figure 2), which roughly falls into 5 130 

QC steps: (1) The component will check the consistency of file(s) according to 131 

filename and md5 code. (2) For genome sequences, the component will check the 132 

legality of genome sequence ID and sequence content, e.g., unique sequence ID, 133 

sequence composition (A/T/C/G or degenerate base), sequence length (≥ 200 bp). (3) 134 

For genome annotations, the component will check gene structure completeness and 135 

consistency, e.g., unique ID, a exon/CDS/UTR coordinate falling within the 136 

corresponding gene coordinate, strand consistency for all features (including 137 

gene/transcript/exon/CDS/UTR), codon validity (e.g., valid start/stop codon, no 138 

internal stop codon). (4) Finally, it will check the internal consistency of genome 139 

sequence and annotation, e.g., sequence ID in genome annotation must match genome 140 

sequence ID, a feature coordinate falling within the range of the corresponding 141 

genome sequence. (5) Genome sequences will also be scanned to check vectors, 142 

adaptors, primers, and indices (collected from UniVec database, 143 

ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/) using NCBI’s VecScreen 144 

(https://www.ncbi.nlm.nih.gov/tools/vecscreen/). If there is an error, a report will be 145 

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automatically sent to the submitter by email. To finish a successful submission, the 146 

submitter needs to fix all errors and resubmit files until they pass the QC process. 147 

Archive and release 148 

GWH will assign a unique accession number to the submitted genome assembly upon 149 

the pass of quality control, allot accession numbers for each genome sequence, gene, 150 

transcript, and protein, generate and backup downloadable files of genome sequence 151 

and annotation in FASTA, GFF3, and TSV formats. Data generation is performed 152 

with in-house-writing scripts based on submitted genome sequence and annotation 153 

files. In order to ensure the security of submitted data, a copy of backup data is stored 154 

on a physically separate disk. GWH will release sequence data on a user-specified 155 

date, unless a paper citing the sequence or accession number is published prior to the 156 

specified release date, in which case the sequence will be released immediately. For 157 

the released data, GWH will generate web pages containing two primary tables: 158 

genome and assembly. The former shows species taxonomy information and genome 159 

assemblies, and the latter contains general information of the assembly (including 160 

external links to other related resources), statistics of genome assembly and its 161 

corresponding annotation. All released data are publicly available at GWH FTP site 162 

(ftp://download.big.ac.cn/gwh/). GWH provides data visualization for both genome 163 

sequence and genome annotation using JBrowse [14]. It offers statistics and charts in 164 

light of total holdings, assembly levels, genome representations, citing articles, 165 

submitting organizations, sequencing platforms, assembly methods, and downloads. 166 

GWH provides user-friendly web interfaces for data browse and query using BIG 167 

Search [13], in order to help users find any released data of interest. For a released 168 

genome assembly, GWH also provides machine-readable APIs (Application 169 

Programming Interfaces) for publicly sharing and automatically obtaining information 170 

on its associated BioProject, BioSample, genome, and assembly metadata and file 171 

paths. 172 

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Global sharing of SARS-CoV-2 and coronavirus genomes  173 

During the COVID-19 outbreak, GWH, in support of the 2019 Novel Coronavirus 174 

Resource (2019nCoVR) [15, 16] has received worldwide submissions of more than a 175 

thousand SARS-CoV-2 genome assemblies with standardized genome annotations 176 

[17], and has released 134 of them. To expand the international influence of data, 62 177 

of the released sequences have been shared, with the submitters’ permission, in 178 

GenBank [18] through a data exchange mechanism established with NCBI. In this 179 

model, GWH accessions are represented as secondary accessions in NCBI GenBank 180 

records, which are retrievable by the NCBI Entrez system. This model sets a good 181 

example for data sharing among different data centers. 182 

In addition, GWH offers sequences of the Coronaviridae family to facilitate 183 

researchers to reach the data conveniently and thus to study the relationship between 184 

SARS-CoV-2 and other coronaviruses. To promote the data sharing and make all 185 

relevant information of the Coronaviridae readily available, GWH integrates genomic 186 

and proteomic sequences as well as their metadata information from NCBI [19], 187 

China National GeneBank Database (CNGBdb) [20], National Microbiology Data 188 

Center (NMDC) [21] and CNCB-NGDC. Duplicated records from different sources 189 

are identified and removed to gain a non-redundant dataset. As of December 31, 2020, 190 

the dataset has 83,095 nucleotide and 575,438 protein sequences of the Coronaviridae. 191 

Filters are implemented to narrow down the required Coronaviridae sequences using 192 

multiple conditions, including country/region, host, isolation source, length, and 193 

collection date. Both the metadata and sequences of the filtered results can be selected 194 

and downloaded as a separate file. The daily updated sequences and all sequences can 195 

also be downloaded from FTP 196 

(ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/). 197 

Data statistics 198 

By December, 2020, GWH has received 17,264 direct submissions covering a broad 199 

diversity of species (Table 1) with different assembly levels (Figure 3). These 200 

genome assemblies link to 301 BioProjects and 16,538 BioSamples, and are 201 

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submitted by 231 submitters from 61 institutions (including 5 international submitters 202 

from 2 countries). There are a total of 3370 released submissions, which were 203 

reported in 83 articles from 44 journals. GWH has over 135,000 visits from 153 204 

countries/regions, with ~891,000 downloads. The amount of data, visits, and 205 

downloads in the GWH has been on the dramatic increase over the past years, clearly 206 

showing its great utility in genome-scale data management. 207 

Summary and future directions 208 

Collectively, GWH is a user-friendly portal for genome data submission, release, and 209 

sharing associated with a matched series of services. The rapid growth of genome 210 

assembly submissions demonstrates the great potential of GWH as an important 211 

resource for accelerating the worldwide genomic research. With the aim to fully 212 

realize the findability, accessibility, interoperability, and reusability (FAIR) of 213 

genome data [22], GWH has made ongoing efforts, including but not limited to, 214 

improvement of web interfaces for data submission, presentation, and visualization, 215 

continuous integration of newly sequenced genomes, and development of useful 216 

online tools to help users analyse genome data (such as BLAST [23]). Therefore, we 217 

will put in more efforts to provide genome annotation services, especially for bacteria 218 

and archaea genomes, with the particular consideration that uniform standardized 219 

annotation determines the accuracy of downstream data analysis. Besides, we will 220 

expand the Coronaviridae dataset to other important pathogens to improve the ability 221 

of public health emergency response. Finally, we plan to share and exchange all 222 

public genome assembly data with the INSDC members to provide comprehensive 223 

data for researchers globally. 224 

CRediT author statement 225 

Meili Chen: Methodology, Software, Investigation, Data Curation, Writing - Original 226 

Draft, Project administration. Yingke Ma: Software, Writing - Original Draft. Song 227 

Wu: Software, Data Curation. Xinchang Zheng: Data Curation. Hongen Kang: 228 

Software. Jian Sang: Investigation, Data Curation. Xingjian Xu: Software. Lili Hao: 229 

Investigation. Zhaohua Li: Data Curation. Zheng Gong: Data Curation. Jingfa Xiao: 230 

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Writing - Review & Editing. Zhang Zhang: Writing - Review & Editing. Wenming 231 

Zhao: Writing - Review & Editing. Yiming Bao: Conceptualization, Writing - 232 

Review & Editing, Supervision. 233 

Competing interests 234 

The authors have declared no competing interests. 235 

Acknowledgments 236 

We thank Profs. Jingchu Luo and Weimin Zhu for their helpful suggestions and a 237 

number of users for reporting bugs and sending comments. We also thank the NCBI 238 

GenBank group, especially Ilene Mizrachi, Karen Clark, Mark Cavanaugh, and Linda 239 

Yankie, for their valuable advices on sequence contamination scanning and 240 

SARS-CoV-2 sequence exchange. This work was supported by Strategic Priority 241 

Research Program of Chinese Academy of Sciences [XDB38060100 and 242 

XDB38030200 to YB; XDB38050300 to WZ; XDB38030400 to JX; XDA19050302 243 

to ZZ]; National Key Research and Development Program of China 244 

[2016YFE0206600 to YB; 2020YFC0847000, 2018YFD1000505, 2017YFC1201202, 245 

and 2016YFC0901603 to WZ; 2017YFC0907502 to ZZ]; The 13th Five-year 246 

Informatization Plan of Chinese Academy of Sciences [XXH13505-05 to YB]; 247 

Genomics Data Center Construction of Chinese Academy of Sciences 248 

[XXH-13514-0202 to YB]; Open Biodiversity and Health Big Data Initiative of IUBS 249 

[to YB]; The Professional Association of the Alliance of International Science 250 

Organizations [ANSO-PA-2020-07 to YB]; National Natural Science Foundation of 251 

China [32030021 and 31871328 to ZZ];  International Partnership Program of the 252 

Chinese Academy of Sciences [153F11KYSB20160008 to ZZ]. 253 

ORCID 254 

ORCID: 0000-0003-0102-0292 (Chen Meili) 255 

ORCID: 0000-0002-9460-4117 (Ma Yingke) 256 

ORCID: 0000-0002-0923-639X (Wu Song) 257 

ORCID: 0000-0001-5739-861X (Zheng Xinchang) 258 

ORCID: 0000-0002-9581-1329 (Kang Hongen) 259 

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ORCID: 0000-0003-4953-3417 (Sang Jian) 260 

ORCID: 0000-0002-4466-3821 (Xu Xingjian) 261 

ORCID: 0000-0003-3432-7151 (Hao Lili) 262 

ORCID: 0000-0002-2673-0103 (Li Zhaohua) 263 

ORCID: 0000-0001-7285-2630 (Gong Zheng) 264 

ORCID: 0000-0002-2835-4340 (Xiao Jingfa) 265 

ORCID: 0000-0001-6603-5060 (Zhang Zhang) 266 

ORCID: 0000-0002-4396-8287 (Zhao Wenming) 267 

ORCID: 0000-0002-9922-9723 (Bao Yiming) 268 

 269 

  270 

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Figure legends 332 

Figure 1  Data model in GWH 333 

Genome assembly accession number is prefixed with "GWH", followed by four 334 

capital letters (represented by XXXX) and 8 zeros. For genome sequence accessions, 335 

eight digits increase in order. For gene sequence, transcript sequence, and protein 336 

sequence accessions, G, T, and P are followed by the GWH prefix, respectively, with 337 

six digits at the end that increase in order. 338 

Figure 2  Major components in GWH data processing workflow 339 

Figure 3  Statistics of genome assembly in GWH (as of December 31, 2020) 340 

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Tables 341 

Table 1  Total data holdings in GWH 342 

Status Type Animals Plants Fungi Bacteria Archaea Viruses Metagenomes Others Total 

Released 
Assembly 

187 
(5.55%) 

210 
(6.23%) 

13 
(0.39%)

220 
(6.53%) 

73 
(2.17%) 

701 
(20.80%)

1957 
(58.07%) 

9 
(0.27%)

3370 

Species 
72 

(19.41%) 
139 

(37.47%) 
12 

(3.23%)
106 

(28.57%) 
11 

(2.96%) 
19 

(5.12%)
3 

(0.81%) 
9 

(2.43%)
371 

Unpublic 
Assembly 

6783 
(48.82%) 

926 
(6.66%) 

5 
(0.04%)

68 
(0.49%) 

13 
(0.09%) 

939 
(6.76%)

4702 
(33.84%) 

458 
(3.30%)

13,894 

Species 
22 

(3.67%) 
549 

(91.50%) 
5 

(0.83%)
7 

(1.17%) 
2 

(0.33%) 
6 

(1.00%)
5 

(0.83%) 
4 

(0.67%)
600 

Total 
Assembly 

6970 
(40.37%) 

1136 
(6.58%) 

18 
(0.10%)

288 
(1.67%) 

86 
(0.50%) 

1640 
(9.50%)

6659 
(38.57%) 

467 
(2.71%)

17,264 

Species 
92 

(9.69%) 
675 

(71.13%) 
16 

(1.69%)
110 

(11.59%) 
13 

(1.37%) 
24 

(2.53%)
7 

(0.74%) 
12 

(1.26%)
949 

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