FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies

High frequency acoustic modes in liquid gallium at the melting point

The microscopic dynamics in liquid gallium (l-Ga) at melting (T=315 K) has been studied by inelastic x-ray scattering. We demonstrate the existence of collective acoustic-like modes up to wave-vectors above one half of the first maximum of the static structure factor, at variance with earlier results from inelastic neutron scattering data [F.J. Bermejo et al. Phys. Rev. E 49, 3133 (1994)]. Despite the structural (an extremely rich polymorphism and rather complex phase diagram) and electronic (mixed valence) peculiarity of l-Ga, its collective dynamics is strikingly similar to the one of Van der Walls and alkali metals liquids. This result speaks in favor of the universality of the short time dynamics in monatomic liquids rather than of system-specific dynamics.Comment: LaTex format, 11 pages, 4 EncapsulatedPostScript figure

Electron-phonon interaction in n-doped cuprates: an Inelastic X-ray Scattering study

Inelastic x-ray scattering (IXS) with very high (meV) energy resolution has become a valuable spectroscopic tool, complementing the well established coherent inelastic neutron scattering (INS) technique for phonon dispersion investigations. In the study of crystalline systems IXS is a viable alternative to INS, especially in cases where only small samples are available. Using IXS, we have measured the phonon dispersion of Nd_{1.86}Ce_{0.14}CuO_{4+\delta} along the [x,0,0] and [x,x,0] in-plane directions. Compared to the undoped parent compound, the two highest longitudinal optical (LO) phonon branches are shifted to lower energies because of Coulomb-screening effects brought about by the doped charge carriers. An additional anomalous softening of the highest branch is observed around q=(0.2,0,0). This anomalous softening, akin to what has been observed in other compounds, provides evidence for a strong electron-phonon coupling in the electron-doped high-temperature superconductors.Comment: Proceedings of the SATT11 conference, Vietri sul Mare - Italy (March 2002); accepted for publication on Int. J. Mod. Phys.

Evidence of anomalous dispersion of the generalized sound velocity in glasses

The dynamic structure factor, S(Q,w), of vitreous silica, has been measured by inelastic X-ray scattering in the exchanged wavevector (Q) region Q=4-16.5 nm-1 and up to energies hw=115 meV in the Stokes side. The unprecedented statistical accuracy in such an extended energy range allows to accurately determine the longitudinal current spectra, and the energies of the vibrational excitations. The simultaneous observation of two excitations in the acoustic region, and the persistence of propagating sound waves up to Q values comparable with the (pseudo-)Brillouin zone edge, allow to observe a positive dispersion in the generalized sound velocity that, around Q=5 nm-1, varies from 6500 to 9000 m/s: this phenomenon was never experimentally observed in a glass.Comment: 5 pages, 3 figures. To appear in Phys. Rev.

Acoustic Nature of the Boson Peak in Vitreous Silica

New temperature dependent inelastic x-ray (IXS) and Raman (RS) scattering data are compared to each other and with existing inelastic neutron scattering data in vitreous silica (v-SiO_2), in the 300 - 1775 K region. The IXS data show collective propagating excitations up to Q=3.5 nm^-1. The temperature behaviour of the excitations at Q=1.6 nm^-1 matches that of the boson peak found in INS and RS. This supports the acoustic origin of the excess of vibrational states giving rise to the boson peak in this glass.Comment: 10 pages and 4 figure

Crystal-like high frequency phonons in the amorphous phases of solid water

The high frequency dynamics of low- (LDA) and high-density amorphous-ice (HDA) and of cubic ice (I_c) has been measured by inelastic X-ray Scattering (IXS) in the 1-15 nm^{-1} momentum transfer (Q) range. Sharp phonon-like excitations are observed, and the longitudinal acoustic branch is identified up to Q = 8nm^{-1} in LDA and I_c and up to 5nm^{-1} in HDA. The narrow width of these excitations is in sharp contrast with the broad features observed in all amorphous systems studied so far. The "crystal-like" behavior of amorphous ices, therefore, implies a considerable reduction in the number of decay channels available to sound-like excitations which is assimilated to low local disorder.Comment: 4 pages, 3 figure

High frequency longitudinal and transverse dynamics in water

High-resolution, inelastic x-ray scattering measurements of the dynamic structure factor S(Q,\omega) of liquid water have been performed for wave vectors Q between 4 and 30 nm^-1 in distinctly different thermodynamic conditions (T= 263 - 420 K ; at, or close to, ambient pressure and at P = 2 kbar). In agreement with previous inelastic x-ray and neutron studies, the presence of two inelastic contributions (one dispersing with Q and the other almost non-dispersive) is confirmed. The study of their temperature- and Q-dependence provides strong support for a dynamics of liquid water controlled by the structural relaxation process. A viscoelastic analysis of the Q-dispersing mode, associated with the longitudinal dynamics, reveals that the sound velocity undergoes the complete transition from the adiabatic sound velocity (c_0) (viscous limit) to the infinite frequency sound velocity (c_\infinity) (elastic limit). On decreasing Q, as the transition regime is approached from the elastic side, we observe a decrease of the intensity of the second, weakly dispersing feature, which completely disappears when the viscous regime is reached. These findings unambiguously identify the second excitation to be a signature of the transverse dynamics with a longitudinal symmetry component, which becomes visible in the S(Q,\omega) as soon as the purely viscous regime is left.Comment: 28 pages, 12 figure