Hippocampome FAQ
Q: How are data
from different articles linked?
Q: Who is doing
the annotating and review of the knowledge base?
Q: How
frequently is the literature surveyed to update the knowledge base?
Q: For
electrophysiology data, why are rats preferred over mice and other rodent
species?
Q:
How are the definitions in the Neuron Term Portal derived?
Q: Does
Hippocampome.org collaborate with any other web sites?
Q: There is
no mention of gap junctions - will these data be added later?
Q: Which browsers
are formally supported by Hippocampome.org?
A: Although
the main categorization property is axo-dendritic pattern, the secondary
properties listed below are sufficient to uniquely separate neuron types. Such significance is placed on these
secondary properties because they can dramatically affect the behavior of the
type in a neuronal network. In the case of CA1 Axo-axonic cells, they specifically
target the axon initial segments of CA1 Pyramidal cells and ignore any other
targets.
-Primary
neurotransmitter: e.g., CA1 Cajal-Retzius and CA1 Neurogliaform
-Targeting specificity: e.g., CA1 Axo-axonic and CA1 Basket
-Consistently differentiating patterns of biomarkers and/or
electrophysiological properties: e.g., CA1 Basket and CA1 Basket CCK+
A: We curate information on
rodent species; consequently, information from guinea pigs is included. Because this information has been
infrequently encountered, it is sparse in the knowledge base.
Q: How are
data from different articles linked?
A: All
data in Hippocampome.org are linked to a neuron type. This can be accomplished directly by
presentation of a reconstruction, schematic, or text description of the neuron;
or indirectly by a citation that provides such a description. In two special cases, data can be linked in
the absence of a description of the axo-dendritic pattern.
The
special cases rely on identification by other prominent characteristics of the
neuron type: 1. soma location in the principal cell layer for DG Granule and
CA1, CA2, and CA3 Pyramidal neuron types, where they make up 90% or greater of
the cell bodies; and 2. axonal tracts
for DG Granule (mossy fibers) and EC hippocampal projecting types (perforant
path).
A: The
data will be putatively linked to both cell types as long as the formal link
can be made to both.
A: Yes,
it is intentional. We assign the prefix MEC to neurons that have been
characterized solely (or are known to exist predominantly) in the Medial
Entorhinal Cortex, such as layer II spiny stellate cells. Similarly, the prefix
LEC is assigned to lateral entorhinal neurons. In contrast, neurons that are
believed to exist in both the medial and lateral entorhinal cortices are given
the prefix EC.
Q: Who is doing
the annotating and review of the knowledge base?
A: Currently,
the annotation and review of the
knowledge base is performed by the authors of the publication (D. W. Wheeler,
C. M. White, C. L. Rees, A. O. Komendantov, D. J. Hamilton, G. A. Ascoli
"Hippocampome.org: A knowledge base of neuron types in the rodent
hippocampus", under review). In the
future, we will endeavor to include mechanisms for direct input from the user
community.
Q: How
frequently is the literature surveyed to update the knowledge base?
A: The current plans are for quarterly
surveys of the literature. A log will be
kept that tracks which new articles are being considered for inclusion into
Hippocampome.org during a future update.
A: Users can utilize the
Feedback button in the main banner to address new or currently included
articles. In addition, we are
automatically made aware of any PMID for which a user searches that is not in
the knowledge base.
Q: For
electrophysiology data, why are rats preferred over mice and other rodent
species?
A: Although
more rat electrophysiological data than mouse exists in the literature (77% of
the electrophysiological parameters sets were taken from rats, 20% from mice,
and 3% from guinea pigs), Hippocampome.org curates both and has a substantial
amount of mouse information. In the
electrophysiological table for legibility reasons, it is only possible to
display one value. To determine the
display value, we prioritize rat, patch-clamp, and body temperature data. However, clicking on any value will display
all of the information, including any from mouse (and from sharp electrodes,
room temperature, etc.). Moreover, we
have plans to make the species displayed a selectable user option.
Q: How are the definitions in the Neuron Term Portal
derived?
A:
The definitions are
derived from 26 sources: BIOPORTAL, CRISP, Gene Ontology, Hippocampome.org,
MeSH, NCBI Gene, NCBI Protein, Neurolex, Protein Ontology, Allen Brain Atlas,
ChEBI, MBF Bioscience, Medical College of Wisconsin, Merriam-Webster Medical,
NeuroElectro, NIST InChI Trust, Scholarpedia, UTHealth Neuroscience, Wolfram
MathWorld, Cambridge Dictionaries, Macmillan Dictionary, Merriam-Webster
Dictionary, Oxford Dictionaries, TheFreeDictionary, Wikipedia, Wiktionary.
Collaborations
Q: Does
Hippocampome.org collaborate with any other web sites?
A: We
fervently think that scientific progress is significantly expedited by
information sharing. Two examples of
collaborative relations are with NeuroElectro and NIF.
Hippocapome.org shared mined electrophysiological data with
NeuroElectro in May 2014 as a gold standard testbed to help validate the
NeuroElectro automated literature mining protocol. We will continue to monitor
future updates of NeuroElectro content for new additional information related
to hippocampus neurons.
We have given NIF scraping access to our website for
inclusion of Hippocampome.org content in their search portal.
Q: There
is no mention of gap junctions - will these data be added later?
A: Yes,
we are in the early stages of annotation information concerning gap junctions
and other synaptic information, which will be added to Hippocampome.org in
future updates.
Q: Which
browsers are formally supported by Hippocampome.org?
A: Hippocampome.org
formally supports current versions of Firefox, Chrome, Safari, and Explorer.
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