We reached 5,000 publications in the Galaxy Publication Library last week. The library tracks publications that use, extend, implement or reference Galaxy or a Galaxy server. It includes journal articles, theses, and a couple of odds and ends. This milestone is a good opportunity to look at what the library tells us about where the Galaxy project has been, and maybe where it's going too.

The library was started December 2011, when the first 168 galaxy related publications were added and classified using 8 tags. This included all project publications plus every pub that ad hoc literature searches could find at the time. The library started on CiteULike and stayed there until September 2017, when we moved it to Zotero. The library grew to 4500 papers during that time.

The library uses tags to indicate how the publication relates to Galaxy. See below for an explanation and history of the tags.

Publications and Tags Over Time

Year	# Pubs		Meth-ods	Work-bench	Use-Public	Use-Main	Tools	Ref-Public	Use-Local	Is-Galaxy	Cloud	Repro-duci-bility	Oth-er	Shar-ed	Un-known	How-To	Pro-ject	Visu-aliza-tion	Use-Cloud
2005	2			1													1
2006	4			3												1
2007	12		2	7							1					2	2
2008	32		15	12		1				2					2		1	1
2009	52		26	18			3			2			1	1	4	1
2010	107		50	36			1			5			1	1	7	3	5
2011	205		93	70		1	8			16	3	6		8	3	4	6	1
2012	396		196	128	1	3	29		3	15	13	7	9	12	10	12	10	2
2013	499		262	150	16	91	37	10	28	27	22	8	9	22	13	7	6	3	2
2014	733		329	224	59	97	67	28	42	47	40	25	40	23	7	11	7	8	1
2015	920		468	232	137	116	67	51	57	48	48	23	34	23	14	8	11	7	2
2016	1104		567	243	206	113	70	109	72	46	35	43	49	20	14	19	7	9	3
2017	929		541	156	207	107	57	75	71	53	19	53	22	16	18	5	5	4	1
2018	5		4		3			1	1
Total	5000		2553	1280	629	529	339	274	274	261	181	165	165	126	92	73	61	35	9

Trends

Trends in the publication library reflect the trajectory of the Galaxy Project over the last 6 years.

Methods

The most obvious "trend" is that there are a lot of pubs using Galaxy in their methods. Just over half of all the publications mention Galaxy in their methods section. This trend doesn't show any sign of slowing down.

UseMain, UsePublic, UseLocal, and UseCloud

Not all Methods paper say which Galaxy instance(s) they used. But starting in 2013, papers that do mention this are also tagged with UseMain, UsePublic, UseLocal, and/or UseCloud tags (see Tags below for an explanation of all tags).

The relative number of UseMain and UsePublic pubs highlights the increasing availability of publicly accessible Galaxy servers. In 2013-2014, there are 2 1/2 times as many UseMain pubs as UsePublic pubs. In 2015 they were about the same, and in 2016-2017, there are nearly twice as many UsePublic pubs as there are UseMain pubs. This rise reflects the increase in available public servers from 21 servers at the start of 2012 to over 90 servers, and 6 services today.

Reproducibility Rising

The last trend I want to highlight is about Reproducibility. Reproducibility has been a core value of Galaxy since at least 2011. The Reproducibilty topic has seen a nearly 3 fold increase since then. There were 21 pubs in all of 2011-2013, compared to 53 pubs in 2017 thus far and Reproducibility has gone from 2.1% of papers to 5.7% of papers in the same time.

Publications per year

The number of publications that reference Galaxy each year has increased every year since the project started. It took over three and a half years to reach 2,500 publications but only a little over two more years to add the next 2,500 publications.

Journals

The library can also tell us which journals are most popular. Here's the top 20:

Rank	Journal	#
1	PLOS ONE	277
2	BMC Genomics	186
3	Nucleic Acids Research	181
4	Bioinformatics	159
5	BMC Bioinformatics	117
6	Scientific Reports	96
7	PLOS Genetics	63
8	Genome Announcements	56
8	Genome Biology	56
8	Genome Research	56
11	Nature Communications	51
12	Briefings in Bioinformatics	46
13	Proceedings of the National Academy of Sciences	44
14	Molecular Ecology	39
15	Cell	36
16	Future Generation Computer Systems	34
17	PLOS Computational Biology	32
18	Cell Reports	31
18	Nature	31
20	Concurrency and Computation: Practice and Experience	29

Eight of the top ten journals are open access. If you are curious about the remaining 1,045 journals they can be found here.

The 5,000th Pub?

The 5,000th pub is

Variations in oral microbiota associated with oral cancer, Hongsen Zhao, Min Chu, Zhengwei Huang, Xi Yang, Shujun Ran, Bin Hu, Chenping Zhang & Jingping Liang. Scientific Reports 7, Article number: 11773 (2017) doi:10.1038/s41598-017-11779-9

Which is an exemplar 5,000th publication: It's a Methods paper, by far the most popular topic tag; a UsePublic paper, an ascendant topic tag; and a >Huttenhower paper, the most frequently referenced public server tag. And it's open access too. See the paper's zotero entry for more.

The Future

If current trends continue we'll hit 10,000 publications sometime in 2021. Look for the update.

Thanks for using Galaxy,

Dave Clements

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More on Tags

We've used Topic Tags since the beginning of the library to track how publications relate to Galaxy. Since the move to Zotero, we've also added Galaxy Featured Tags, Public Server Tags, and Publisher Tags. They are all explained here.

Topic Tags

Topic tags indicate how the publication relates to Galaxy. Here's the current set and when each tag was added:

Tag	Explanation	Year
+HowTo	Papers about how to use Galaxy for specific analyses. These are tutorials.	2011
+IsGalaxy	Publications about Galaxy itself or installations of Galaxy.	2011
+Methods	Uses Galaxy in their methods.	2011
+Other	Publications that don't fit well under any other tag.	2011
+Project	Publications with a Galaxy team member as an author.	2011
+Reproducibility	Reproducibility and persistence in science.	2011
+Shared	Publications that have published workflows, histories, datasets, pages, or visualizations in a Galaxy instance.	2011
+Workbench	Publication mentions Galaxy as a platform.	2011
+Tools	Tools that run in, have been ported to, or interact with Galaxy	2012
+Cloud	Publications referencing / extending / discussing Galaxy in a cloud context.	2013
+RefPublic	References a publicly accessible Galaxy instance or a Galaxy service. This is distinct from the +UsePublic tag.	2013
+Unknown	Publications that we know refer to Galaxy, but we aren't sure how because they are behind a paywall we don't have access to. These are revisited periodically.	2013
+UseCloud	Uses a custom built cloud based instance of Galaxy in its methods.	2013
+UseLocal	Uses a local installation of Galaxy in its methods.	2013
+UseMain	Uses the project's public server, usegalaxy.org (a.k.a. Main, in its methods.	2013
+UsePublic	Uses a publicly accessible Galaxy instance or a Galaxy service in its methods.	2013
+Visualization	Publications referencing Galaxy in a visualization and/or visual analytics context.	2013

Galaxy Featured Tags

With the move to Zotero we added two new sets of tags. The first set is used to highlight publications that feature Galaxy prominently:

Tag	Explanation
+Galactic	Publication is about Galaxy.
+Stellar	Publication features Galaxy prominently.

Public server and services tags

The second set of new tags show which public Galaxy server or service is used or discussed in publications. These are tagged with the server's name, preceded by a ">". For example, the >RepeatExplorer tag lists all papers that use or reference the RepeatExplorer public server.

Publisher Tags

Zotero is configured to also add any keywords it can detect automatically when the publication is added. These tags are not rationalized in any way, and tend to describe the research topic or domain. Prosapip1 and Genome evolution are examples.

Retroactive Tagging?

These tags were added over a 6 year period. Are older papers back-tagged when new tags are added? Mostly not, but there are some exceptions:

• Galaxy Featured Tags exist back to the beginning of time. (These were converted from CiteULike's priority feature.)
• Topic and Public Server/Service tags have been applied to older publications on a selected basis.

Therefore, don't look for a lot of +UseMain or +Cloud tagged papers from before 2013.