Mary Ann Tuli

*![Bund](http://gigasciencejournal.com/blog/wp-content/uploads/2018/04/IMG_8912-300x225.jpg){.size-medium
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sizes="(max-width: 300px) 100vw, 300px"}GigaScience are regular
attendees of the International Biocuration Conference, and you may have
read our write-ups ups [going back to 2012
edition](http://gigasciencejournal.com/blog/the-state-of-the-curation-nation/). This
year Biocuration is back [behind the bamboo
curtain](http://gigasciencejournal.com/blog/biocuration-behind-bamboo-curtain/),
with the 11th conference held in the Crowne Plaza Hotel Shanghai from
April 8th-11th and hosted by Fudan University.*

*Symbolised by the spectacular Bund waterfront, Shanghai is the very
symbol of modern China, and there was a palpable excitement at this
year's focus on **Big Data Innovation** and the promise to translate Big
Data into biomedical knowledge and understanding. The GigaScience
curation team participated heavily, with Mary Ann Tuli presenting a talk
on "What MODs can learn from Journals -- a GigaDB curator's perspective"
(slides
[here](https://www.slideshare.net/GigaScience/mary-ann-tuli-what-mods-can-learn-from-journals-a-gigadb-curators-perspective)),
and Chris Armit participating in the Translational Data Curation &
Harmonisation panel. Here the team provide a write-up of how the meeting
went.*

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**A Shanghai Biocuration Surprise  
**The Biocuration community work together to ensure data integrity and
consistency in data content. Towards this end, a multitude of tools were
presented that enable data cleaning, data standardisation, and the
addition of metadata sample attributes to ensure that datasets are both
findable and intelligible.

To illustrate with a few example, EMBL-EBI's
*[Annotare](https://code.google.com/archive/p/annotare/)* -- presented
by Anja Füllgrabe -- is a user-friendly web interface that uses forms
enabled with controlled vocabularies and predictive text to help
submitting authors add sample attributes to their *[Array
Express](https://www.ebi.ac.uk/arrayexpress/)* and *[Expression
Atlas](https://www.ebi.ac.uk/gxa/home)* datasets. The sample metadata
can be curated in a tabular *[MAGE-Tab
format](https://www.ebi.ac.uk/arrayexpress/help/magetab_spec.html)*,
ensuring that errors that have been introduced by naïve submitters are
stripped from the metadata prior to publication.

Edith Wong of Stanford University discussed the importance of data
standardisation in the context of the *[Saccharomyces Genome Database
(SGD)](https://www.yeastgenome.org/)* and their move towards presenting
RNA-seq data as molecules per cell rather than as fluorescence units.
The use of standard units in this way is an important means of ensuring
that the vast amount of RNA-seq data that is available is intelligible,
and enables integration and cross-comparison of sequence data derived
from proprietary platforms.

In the **Clinical and Translational Data Curation and Harmonization
Workshop**, Richard Schneider of the Luxembourg Center for Systems
Biomedicine (LCSB) presented a fourfold framework that is pertinently
relevant for the entire Biocuration community. This framework
included: 1) Data format conversion, to a machine-readable format; 2)
Data cleansing, to remove errors, inconsistencies, and ambiguities; 3)
Data transformation, to impute missing data; and 4) Data
standardisation, including the use of controlled vocabularies,
ontologies, and standard units. Many, if not all, of the tools presented
at this year's meeting could be classified within this framework. An
important addition by Suzi Lewis of Lawrence Berkeley National
Laboratory, was to highlight that data cleaning should not be thought of
as limited to metadata, as there are annotation tools available -- such
as *[Apollo](http://genomearchitect.github.io/)* -- that enable direct
curation of sequence data using a graphical and sharable web-based
interface.

Of great interest to the Biocuration community was the development of
automation tools to reduce human intervention and productivity tools
that make human intervention easy as possible. Many of the tools
showcased at the two poster sessions addressed these concerns. In
addition, many of the talks expressed the overarching need for large
data centres to orchestrate, collect and archive large amounts of
biological data. An important initiative in this respect is the *[Elixir
European repository](https://www.elixir-europe.org/),* which promises
10-year sustainability for open data generated in Europe, and provides
high availability of these data through the use of virtual servers.
However, as Martin Romacker of Roche Innovation Center, Basel was quick
to point out, this only applies to open data, and the view from the
industrial sector is that there is a pertinent need for web tools to
analyse patient data that cannot be released due to privacy requirements
for clinical data.

**The Database Resources of the BIG Data Center Workshop** was
particularly insightful in this respect. The core resources in the BIGD
are genome sequence archive, genome warehouse, gene expression nebulas,
genome variation map, methylation bank, and science wikis (wikis for
community annotations). The *[BIGD Genome
Warehouse](http://bigd.big.ac.cn/gwh/)* is a repository for whole genome
sequence (WGS) data and currently archives 157 human genomes (496 TB
data), although for privacy reasons these are not accessible from the
Genome Warehouse web interface. BIGD propose to deliver a web-based
Blast sequence alignment tool capable of handling WGS data, and this
represents an important means of assessing sequence similarity between
human genomic datasets, whilst respecting privacy agreements. An
alternative solution was provided by [Genomics
England](https://www.genomicsengland.co.uk/) -- represented by this
year's Biocuration Career Award winner Eleanor Williams -- which
provides a *[Gene Panel App](https://panelapp.genomicsengland.co.uk/)*
to assess gene variants likely to be associated with rare diseases and
cancer. These represent important initiatives that aim to analyse human
data, whilst ensuring that the original genomic datasets remain private
and confidential.

Our favourite topic of **Open Data** was a major focus at this
conference. The [*FAIR princi*ples](https://www.dtls.nl/fair-data/) --
that ensure research data is Findable, Accessible, Interoperable and
Reusable -- was an overarching theme for many of the talks, indicating
that these principles are well supported within the MODs and other
resources. An intriguing study in this respect was provided by the
(Re)usable Data Project -- presented by Lilly Winfree of Oregon Health
and Science University -- that highlighted how complex licensing and
data reuse restrictions are hindering the reuse of seemingly 'open'
data. These complexities can range from alternative  *[Creative Common
Licenses](https://creativecommons.org/licenses/)* (CC-BY, CC-ND, CC-NC,
etc) being used for data subsets in a single data resource, to terms of
use on the website that contradict the stated license agreement. The
(Re)usable Data Project developed a five-part rubric to evaluate and
rank over 50 biomedical and biological data resources, and a key finding
of this study was that over 50% of data resources lacked a clear and
easily findable license. This highlights a clear need to improve
licensing practices so as to enable data reuse by the research
community.

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Mary Ann Tuli, Chris Armit and "Jesse" Xiao Si Zhe from the GigaDB team.
:::

**The Careers in Biocuration Workshop** was of great interest to this
community. There was a general lack of support for remote working,
although as Mary Ann Tuli pointed out this model worked very well for
our "Big Data" Journal
*[GigaScience](http://www.gigasciencejournal.com)*. To understand the
hopes, dreams, and skillsets of the biocurator community, the
Biocuration Career Description Survey queried the background,
computational skills, and career satisfaction of the workshop attendees.

The results of this survey *[are available on the ISB
website](https://www.biocuration.org/dissemination/survey-results/) *
and will be used to better inform scientists, students, and newcomers to
Biocuration as a career path. A white paper "Biocuration: Distilling
data into knowledge" was additionally discussed as a critical means of
increasing public awareness on the key role biocuration plays in
scientific discovery.

Training opportunities for Biocurators was an additional topic of great
interest. The Institute of Continuing Education at Cambridge University
will be providing a [one-year PgCert in
Biocuration](https://www.ice.cam.ac.uk/course/postgraduate-certificate-biocuration)
from September/October 2018. The course will be mostly online but will
additionally include face-to-face sessions and is deemed suitable for
both new and experienced biocurators.

The post [Biocuration on the
Bund](http://gigasciencejournal.com/blog/biocuration-on-the-bund/){rel="nofollow"}
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[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<em>
 GigaScience are regular attendees of the International Biocuration Conference, and you may have read our write-ups ups going back to 2012 edition. This year Biocuration is back behind the bamboo curtain, with the 11th conference held in the Crowne Plaza Hotel Shanghai from April 8th-11th and hosted by Fudan University.
</em>
<em>
 Symbolised by the spectacular Bund waterfront, Shanghai is the very symbol of modern China, and there was a
</em>

Rogue Scholar Posts

Biocuration on the Bund