BMC Bioinformatics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: Dec. 14, 2023
Abstract
Background
The
standardization
of
biological
data
using
unique
identifiers
is
vital
for
seamless
integration,
comprehensive
interpretation,
and
reproducibility
research
findings,
contributing
to
advancements
in
bioinformatics
systems
biology.
Despite
being
widely
accepted
as
a
universal
identifier,
scientific
names
species
have
inherent
limitations,
including
lack
stability,
uniqueness,
convertibility,
hindering
their
effective
use
databases,
particularly
natural
product
(NP)
occurrence
posing
substantial
obstacle
utilizing
this
valuable
large-scale
applications.
Result
To
address
these
challenges
facilitate
high-throughput
analysis
involving
names,
we
developed
PhyloSophos,
Python
package
that
considers
the
properties
taxonomic
accurately
map
name
inputs
entries
within
chosen
reference
database.
We
illustrate
importance
assessing
multiple
databases
considering
syntax-based
pre-processing
NP
an
example,
with
ultimate
goal
integrating
heterogeneous
information
into
single,
unified
dataset.
Conclusions
anticipate
PhyloSophos
significantly
aid
systematic
processing
poorly
digitized
curated
data,
such
biodiversity
ethnopharmacological
resources,
enabling
full-scale
resources.
Australian Mammalogy,
Journal Year:
2022,
Volume and Issue:
45(1), P. 13 - 23
Published: Oct. 12, 2022
The
use
of
correct
taxonomy
to
describe
and
name
the
earth’s
biodiversity
is
fundamental
conservation
management.
However,
there
are
issues
that
need
be
overcome
ensure
described
taxa
their
scientific
names
both
appropriate
widely
adopted.
Obstacles
this
include
different
species
definitions,
taxonomic
instability
due
accumulation
additional
specimens
in
analyses
progression
science
allows
better
resolution
boundaries,
inappropriate
description
naming
new
without
adequate
basis
self-published
journals
(known
as
‘taxonomic
vandalism’).
In
an
effort
manage
instability,
Australasian
Mammal
Taxonomy
Consortium
(AMTC),
affiliated
body
Australian
Society,
has
developed
several
tools
include:
(1)
a
standardised
list
mammal
common
names;
(2)
recommendations
for
information
should
included
published
descriptions;
(3)
support
publication
aspidonyms
(i.e.
scientifically
acceptable
proposed
overwrite
pre-existing
unscientific
name).
This
review
discusses
these
issues,
reaffirms
foundations
research,
provides
guidelines
those
publishing
research
on
mammals.
Frontiers in Ecology and Evolution,
Journal Year:
2023,
Volume and Issue:
11
Published: March 16, 2023
Plant
and
animal
checklists,
with
conservation
status
information,
are
fundamental
for
management.
Historical
field
data,
more
recent
data
of
digital
origin
data-sharing
platforms
provide
useful
sources
collating
species
locality
data.
However,
different
biodiversity
datasets
have
formats
inconsistent
naming
systems.
Additionally,
most
do
not
an
easy
option
download
by
protected
area.
Further,
data-entry-ready
software
is
readily
available
organization
staff
limited
technical
skills
to
collate
these
heterogeneous
create
distribution
maps
checklists
areas.
The
insights
presented
here
the
outcome
conceptualizing
a
information
system
South
African
National
Parks.
We
recognize
that
requirement
achieving
better
standardization,
sharing
use
capacity
building,
internet
connectivity,
national
institutional
management
support
collaboration.
focus
on
some
issues
need
be
considered
standardization
support.
outline
using
taxonomic
backbones
standardizing
utility
from
Global
Biodiversity
Information
Facility
other
in
this
process.
we
make
recommendations
fields
needed
relational
databases
can
used
inform
decisions
steps
taken
enable
easier
collation
Africa
as
case
study.
Proceedings of the National Academy of Sciences,
Journal Year:
2023,
Volume and Issue:
120(45)
Published: Oct. 30, 2023
Taxonomic
data
are
a
scientific
common.
Unlike
nomenclature,
which
has
strong
governance
institutions,
there
currently
no
generally
accepted
institutions
for
the
compilation
of
taxonomic
into
an
global
list.
This
gap
results
in
challenges
conservation,
ecological
research,
policymaking,
international
trade,
and
other
areas
societal
importance.
Consensus
on
list
its
management
requires
effective
standards,
including
agreed
mechanisms
choosing
among
competing
taxonomies
partial
lists.
However,
frameworks
lacking,
call
2017
generated
critical
responses.
Any
system
to
compliance
is
voluntary
high
level
legitimacy
credibility
those
by
whom
it
created.
Legitimacy
credibility,
turn,
require
adequate
credible
consultation.
Here,
we
report
survey
taxonomists,
scientists
from
disciplines,
users
taxonomy
designed
assess
views
test
ideas
new
governance.
We
found
surprisingly
degree
agreement
need
species
their
names,
consistent
what
such
should
provide
how
be
governed.
The
suggests
that
consensus
mechanism
create,
manage,
govern
single
widely
all
world’s
achievable.
finding
was
unexpected
given
past
controversies
about
merits
Annals of Botany,
Journal Year:
2023,
Volume and Issue:
133(5-6), P. 789 - 800
Published: July 28, 2023
Taxonomists
are
primary
actors
of
biodiversity
assessment.
At
the
same
time,
there
is
awareness
by
taxonomic
community
at
large
that
field
going
through
a
crisis,
sometimes
referred
to
as
'taxonomic
impediment'.
Coupled
with
ongoing
or
6th
mass
extinction,
this
impedance
puts
risk
target
set
in
Convention
on
Biological
Diversity's
(CBD)
Global
Biodiversity
Framework
vision
2050,
which
calls
for
urgent
action
'…
put
path
recovery
2030
benefit
planet
and
people'.
This
particularly
pronounced
tropical
African
countries
where
studies
done
an
ad
hoc
basis.
In
study,
our
aim
investigate
historical
trends
botanical
exploration
vascular
plants
Nigeria
forecast
near-term
(50-year)
description
presently
unknown
species,
we
use
discuss
scenarios
effort
may
be
necessary
comprehensive
assessment
country.
Taxon,
Journal Year:
2023,
Volume and Issue:
72(5), P. 1137 - 1142
Published: Oct. 1, 2023
Abstract
A
Special‐purpose
Committee
on
DNA
Sequences
as
Types
was
established
at
the
XIX
International
Botanical
Congress
(IBC)
in
Shenzhen,
China
2017,
with
a
mandate
to
report
XX
IBC
recommendations
preferred
course
of
action
respect
sequences
potential
types
under
Code
Nomenclature
for
algae,
fungi,
and
plants
.
This
provides
synthesis
deliberations
from
this
issue.
We
discuss
two
options
dealing
problem
that
many
species,
especially
microfungi
microalgae,
can
be
discovered
delimited
using
eDNA
sequencing
but
cannot
currently
formally
named
due
requirement
either
specimen
or
illustration
nominated
holotype.
One
option
is
expand
definition
“type”
include
sequences,
while
second
would
allow
some
taxa
without
types,
application
their
names
instead
being
determined
sequence.
should
read
concert
formal
proposals
amendments
effect
these
options,
published
issue
Taxon
Open Mind,
Journal Year:
2024,
Volume and Issue:
8, P. 102 - 130
Published: Jan. 1, 2024
Abstract
Categorization
is
ubiquitous
in
human
cognition
and
society,
shapes
how
we
perceive
understand
the
world.
Because
categories
reflect
needs
perspectives
of
their
creators,
no
category
system
entirely
objective,
inbuilt
biases
can
have
harmful
social
consequences.
Here
propose
methods
for
measuring
hierarchical
systems
categories,
a
common
form
organization
with
multiple
levels
abstraction.
We
illustrate
these
by
quantifying
extent
to
which
library
classification
are
biased
favour
western
concepts
male
authors.
analyze
large
data
set
including
more
than
3
million
books
organized
into
thousands
find
that
related
religion
show
greater
bias
do
literature
or
history,
written
men
distributed
broadly
across
women.
also
Dewey
Decimal
Classification
shows
level
does
Library
Congress
Classification.
Although
focus
on
as
case
study,
our
general,
be
used
measure
both
natural
institutional
range
domains.1
European Journal of Taxonomy,
Journal Year:
2024,
Volume and Issue:
943
Published: July 17, 2024
Species
lists
play
an
important
role
in
biology
and
practical
domains
like
conservation,
legislation,
biosecurity
trade
regulation.
However,
their
effective
use
by
non-specialist
scientific
societal
users
is
sometimes
hindered
disagreements
between
competing
lists.
While
it
well-known
that
such
exist,
remains
unclear
how
prevalent
they
are,
what
nature
is,
causes
them.
In
this
study,
we
argue
these
questions
should
be
investigated
using
methods
based
on
taxon
concept
rather
than
Linnaean
names,
a
concept-based
method
to
quantify
disagreement
about
bird
classification
investigate
its
relation
research
effort.
We
found
there
was
38%
of
all
groups
birds
recognized
as
species,
more
three
times
much
indicated
previous
measures.
Disagreement
the
delimitation
most
common
kind
conflict,
outnumbering
nomenclature
rank.
high
levels
conflict
rank
were
associated
with
lower
effort,
not
case
for
groups.
This
suggests
taxonomic
cannot
resolved
simply
increasing
European Journal of Taxonomy,
Journal Year:
2023,
Volume and Issue:
908
Published: Nov. 15, 2023
Taxonomic
criteria
alone
are
not
sufficient
to
determine
a
linear
sequence
for
the
arrangement
of
collection
specimens
according
preferred
classification
or
which
taxa
best
discussed
in
articles
books.
The
choice
methodology
obtain
agreement
with
hierarchical
has
been
little
studied
and
remains
controversial.
In
this
article,
I
offer
an
historical
background,
before
examining
properties,
use
limits
possible
listing
criteria.
result
linearization
effort
depends
on
arbitrary
choices
respect
two
aspects
we
intend
linearize.
One
is
order
be
followed
immediately
subordinate
members
given
taxon,
other
sets
linearized
tradition,
alphabetic
criterion.
example
presented
here,
related
“orders”
Hexapoda,
demonstrates
need
specify
very
clearly
extent
composition
uncollapsed
backbone
retained
procedure.
F1000Research,
Journal Year:
2022,
Volume and Issue:
10, P. 1238 - 1238
Published: Aug. 1, 2022
Threats
to
global
biodiversity
are
increasingly
recognised
by
scientists
and
the
public
as
a
critical
challenge.
Molecular
sequencing
technologies
offer
means
catalogue,
explore,
monitor
richness
biogeography
of
life
on
Earth.
However,
exploiting
their
full
potential
requires
tools
that
connect
infrastructures
resources.
As
research
infrastructure
developing
services
technical
solutions
help
integrate
coordinate
science
resources
across
Europe,
ELIXIR
is
key
player.
To
identify
opportunities,
highlight
priorities,
aid
strategic
thinking,
here
we
survey
approaches
which
molecular
inform
understanding
biodiversity.
We
detail
example
use
cases
how
DNA
is:
resolving
taxonomic
issues;
Increasing
knowledge
marine
biodiversity;
helping
understand
agriculture
critically
linked;
playing
an
essential
role
in
ecological
studies.
Together
with
examples
national
programmes,
show
where
progress
being
made
but
also
common
challenges
opportunities
for
future
enhancement
underlying
wider
domains.
Based
emerging
themes,
propose
recommendations
guide
funding
research:
bioinformatic
need
collaborate
closely
strategically;
efforts
be
aligned
harmonised
domains;
metadata
needs
standardised
data
management
widely
adopted;
current
scaled
up
dramatically
address
anticipated
explosion
data;
bioinformatics
support
enabled
sustained;
training
end
users
prioritised;
community
initiatives
proactive
focused
enabling
solutions.
For
deliver
they
must
connected
knowledge:
together,
sequence
collection
can
advance
prevent
further
decline
Earth’s
biodiversity.