Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

Background: Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results: We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion: We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation

Search for CPCP violation in the D+→π+π0D^{+}\to\pi^{+}\pi^{0} decay at Belle

We search for $CP$ violation in the charged charm meson decay $D^{+}\to\pi^{+}\pi^{0}$, based on a data sample corresponding to an integrated luminosity of $\rm 921~fb^{-1}$ collected by the Belle experiment at the KEKB $e^{+}e^{-}$ asymmetric-energy collider. The measured $CP$ violating asymmetry is $[+2.31\pm1.24({\rm stat})\pm0.23({\rm syst})]\%$, which is consistent with the standard model prediction and has a significantly improved precision compared to previous results.Comment: 8 pages, 3 figure

First observation of the hadronic transition Υ(4S)→ηhb(1P) \Upsilon(4S) \to \eta h_{b}(1P) and new measurement of the hb(1P)h_b(1P) and ηb(1S)\eta_b(1S) parameters

Using a sample of $771.6 \times 10^{6}$ $\Upsilon(4S)$ decays collected by the Belle experiment at the KEKB $e^+e^-$ collider, we observe for the first time the transition $\Upsilon(4S) \to \eta h_b(1P)$ with the branching fraction ${\cal B}[\Upsilon(4S) \to \eta h_b(1P)]= (2.18 \pm 0.11 \pm 0.18) \times 10^{-3}$ and we measure the $h_b(1P)$ mass $M_{h_{b}(1P)} = (9899.3 \pm 0.4 \pm 1.0)$ MeV/$c^{2}$, corresponding to the hyperfine splitting $\Delta M_{\mathrm HF}(1P) = (0.6 \pm 0.4 \pm 1.0)$ MeV/$c^{2}$. Using the transition $h_b(1P) \to \gamma \eta_b(1S)$, we measure the $\eta_b(1S)$ mass $M_{\eta_{b}(1S)} = (9400.7 \pm 1.7 \pm 1.6)$ MeV/$c^{2}$, corresponding to $\Delta M_{\mathrm HF}(1S) = (59.6 \pm 1.7 \pm 1.6)$ MeV/$c^{2}$, the $\eta_b(1S)$ width $\Gamma_{\eta_{b}(1S)} = (8 ^{+6}_{-5} \pm 5)$ MeV/$c^{2}$ and the branching fraction ${\cal B}[h_b(1P) \to \gamma \eta_b(1S)]= (56 \pm 8 \pm 4) \%$.Comment: 7 pages, 2 figures, submitted to Phys. Rev. Let

Linguistic feature analysis for protein interaction extraction

<p>Abstract</p> <p>Background</p> <p>The rapid growth of the amount of publicly available reports on biomedical experimental results has recently caused a boost of text mining approaches for protein interaction extraction. Most approaches rely implicitly or explicitly on linguistic, i.e., lexical and syntactic, data extracted from text. However, only few attempts have been made to evaluate the contribution of the different feature types. In this work, we contribute to this evaluation by studying the relative importance of deep syntactic features, i.e., grammatical relations, shallow syntactic features (part-of-speech information) and lexical features. For this purpose, we use a recently proposed approach that uses support vector machines with structured kernels.</p> <p>Results</p> <p>Our results reveal that the contribution of the different feature types varies for the different data sets on which the experiments were conducted. The smaller the training corpus compared to the test data, the more important the role of grammatical relations becomes. Moreover, deep syntactic information based classifiers prove to be more robust on heterogeneous texts where no or only limited common vocabulary is shared.</p> <p>Conclusion</p> <p>Our findings suggest that grammatical relations play an important role in the interaction extraction task. Moreover, the net advantage of adding lexical and shallow syntactic features is small related to the number of added features. This implies that efficient classifiers can be built by using only a small fraction of the features that are typically being used in recent approaches.</p

Observation of the Radiative Decays of ψ (1S) to χc1

© 2020 authors. Published by the American Physical Society. We report the first observation of the radiative decay of the ψ(1S) into a charmonium state. The significance of the observed signal of ψ(1S)→γχc1 is 6.3 standard deviations including systematics. The branching fraction is calculated to be B[ψ(1S)→γχc1]=[4.7-1.8+2.4(stat)-0.5+0.4(sys)×10-5]. We also searched for ψ(1S) radiative decays into χc0,2 and ηc(1S,2S), and set upper limits on their branching fractions. These results are obtained from a 24.9 fb-1 data sample collected with the Belle detector at the KEKB asymmetric-energy e+e- collider at a center-of-mass energy equal to the ψ(2S) mass using ψ(1S) tagging by the ψ(2S)→ψ(1S)π+π- transitions

Search for B+ -> l+ nu gamma decays with hadronic tagging using the full Belle data sample

We search for the decay B+ -> l+ nu gamma with l+ = e+ or mu+ using the full Belle data set of 772 x 10^6 BBbar pairs, collected at the Y(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e- collider. We reconstruct one B meson in a hadronic decay mode and search for the B+ -> l+ nu gamma decay in the remainder of the event. We observe no significant signal within the phase space of E_gamma^sig > 1 GeV and obtain upper limits of BR(B+ -> e+ nu gamma) mu+ nu gamma) l+ nu gamma) < 3.5 x 10^-6 at 90 % credibility level.Comment: Submitted to Phys. Rev.

Observation of an alternative χc0(2P)\chi_{c0}(2P) candidate in e+e−→J/ψDDˉe^+ e^- \rightarrow J/\psi D \bar{D}

We perform a full amplitude analysis of the process $e^+ e^- \rightarrow J/\psi D \bar{D}$, where $D$ refers to either $D^0$ or $D^+$. A new charmoniumlike state $X^*(3860)$ that decays to $D \bar{D}$ is observed with a significance of $6.5\sigma$. Its mass is ($3862^{+26}_{-32}{}^{+40}_{-13}$) MeV/$c^2$ and width is ($201^{+154}_{-67}{}^{+88}_{-82}$) MeV. The $J^{PC}=0^{++}$ hypothesis is favored over the $2^{++}$ hypothesis at the level of $2.5\sigma$. The analysis is based on the 980 $\mathrm{fb}^{-1}$ data sample collected by the Belle detector at the asymmetric-energy $e^+ e^-$ collider KEKB.Comment: 17 pages, 11 figure

Inclusive cross sections for pairs of identified light charged hadrons and for single protons in e+e−e^+e^- at s=\sqrt{s}= 10.58 GeV

We report the first double differential cross sections of two charged pions and kaons ($e^+e^- \rightarrow hhX$) in electron-positron annihilation as a function of the fractional energies of the two hadrons for any charge and hadron combination. The dependence of these di-hadron cross sections on the topology (same, opposite-hemisphere or anywhere) is also studied with the help of the event shape variable thrust and its axis. The ratios of these di-hadron cross sections for different charges and hadron combinations directly shed light on the contributing fragmentation functions. For example, we find that the ratio of same-sign pion pairs over opposite-sign pion pairs drops toward higher fractional energies where disfavored fragmentation is expected to be suppressed. These di-hadron results are obtained from a $655\,{\rm fb}^{-1}$ data sample collected near the $\Upsilon(4S)$ resonance with the Belle detector at the KEKB asymmetric-energy $e^+ e^-$ collider. Extending the previously published single-pion and single-kaon cross sections, single-proton ($e^+e^- \rightarrow pX$) cross sections are extracted from a $159\,{\rm fb}^{-1}$ data sub-sample.Comment: submitted to PR